Untitled
Ethan Tolman
2023-11-02
#############Making Maps###################
#install.packages("devtools")
#devtools::install_github("cmt2/RevGadgets")
library(RevGadgets)
library(coda)
library(ggplot2)
library(ggtree)## ggtree v3.10.0 For help: https://yulab-smu.top/treedata-book/
##
## If you use the ggtree package suite in published research, please cite
## the appropriate paper(s):
##
## Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
## ggtree: an R package for visualization and annotation of phylogenetic
## trees with their covariates and other associated data. Methods in
## Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
##
## Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan
## Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. Ggtree: A serialized data
## object for visualization of a phylogenetic tree and annotation data.
## iMeta 2022, 1(4):e56. doi:10.1002/imt2.56
##
## S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L
## Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact
## visualization of richly annotated phylogenetic data. Molecular Biology
## and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166library(grid)
library(gridExtra)
library(ggplot2)
library(maps)
library(readr)
library(dplyr)##
## Attaching package: 'dplyr'## The following object is masked from 'package:gridExtra':
##
## combine## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionlibrary(RColorBrewer)######deltaGLS (gene likelihood scores) test######
library(ggplot2)
library(grid)
library(gridExtra)
likelihoods <- read.table("gene_likelihoods.tsv", head =T, sep="\t")
likelihoods$Petalura_vs_Uropetala <- likelihoods$Petalura_out - likelihoods$Uropetala_out
likelihoods$Petalura_vs_Phenes <- likelihoods$Petalura_out - likelihoods$Phenes_out
likelihoods$Phenes_vs_Uropetala <- likelihoods$Phenes_out - likelihoods$Uropetala_out
likelihoods$ingentissima_vs_gigantea <- likelihoods$Phenes_out - likelihoods$hesperia_alternate
likelihoods$ingentissima_vs_out <- likelihoods$Phenes_out - likelihoods$hesperia_out
likelihoods$gigantea_vs_out <- likelihoods$hesperia_alternate - likelihoods$hesperia_out
likelihoods <- likelihoods[order(likelihoods$Petalura_vs_Uropetala),]
likelihoods$orders<-1:length(likelihoods$Petalura_vs_Uropetala)
likelihoods$col <- likelihoods$Petalura_out
for (x in 1:length(likelihoods$Petalura_out)) {
if(likelihoods$Petalura_vs_Uropetala[[x]] < 0){
likelihoods$col[x] <- "Uropetala"
}else if (likelihoods$Petalura_vs_Uropetala[[x]] > 0){
likelihoods$col[x] <- "Petalura"
}else{
likelihoods$col[x] <- "Relationships are\nequally likely"
}
}
ggplot(likelihoods, aes(x=orders, y=Petalura_vs_Uropetala, color = col)) + geom_point(size=2) + scale_color_brewer(palette="Dark2") + theme_minimal()+geom_hline(yintercept=0) +labs(y="Likelihood of Outgroup",x="") +
labs(title = "Supported Outgroup of Gondwanan Clade") + theme(plot.title = element_text(hjust = 0.5, face = "bold.italic", size = 20)) + labs(color = "Supported Outgroup") + theme(legend.text=element_text(size=12, face = "italic")) + theme(legend.title=element_text(size=15)) + guides(colour = guide_legend(override.aes = list(size=10))) + theme(text = element_text(family = "Times New Roman"))
likelihoods <- likelihoods[order(likelihoods$Petalura_vs_Phenes),]
likelihoods$orders<-1:length(likelihoods$Petalura_out)
for (x in 1:length(likelihoods$Petalura_out)) {
if(likelihoods$Petalura_vs_Phenes[[x]] < 0){
likelihoods$col[x] <- "Phenes"
}else if (likelihoods$Petalura_vs_Phenes[[x]] > 0){
likelihoods$col[x] <- "Petalura"
}else{
likelihoods$col[x] <- "Relationships are\nequally likely"
}
}
ggplot(likelihoods, aes(x=orders, y=Petalura_vs_Phenes, color = col)) + geom_point(size=2) + scale_color_brewer(palette="Dark2") + theme_minimal()+geom_hline(yintercept=0) +labs(y="Likelihood of Outgroup",x="") +
labs(title = "Supported Outgroup of Gondwanan Clade") + theme(plot.title = element_text(hjust = 0.5, face = "bold.italic", size = 20)) + labs(color = "Supported Outgroup") + theme(legend.text=element_text(size=12, face = "italic")) + theme(legend.title=element_text(size=15)) + guides(colour = guide_legend(override.aes = list(size=10))) + theme(text = element_text(family = "Times New Roman"))
#pet_v_phen_lm <- lm(Petalura_vs_Phenes ~ chromosome + mean_substitution_rate + chromosome*mean_substitution_rate, data = likelihoods)
#Get the model residuals
#model_residuals = pet_v_phen_lm$residuals
#Plot the residuals
#qqnorm(model_residuals)
#Plot the Q-Q line
#qqline(model_residuals)
#summary(pet_v_phen_lm)
print(c(likelihoods$Petalura_out, likelihoods$Phenes_out))## [1] -146.20874 -169.44146 -177.71388 -148.81612 -115.50141 -147.98243
## [7] -149.72151 -182.24006 -176.96057 -134.76466 -178.60696 -163.29787
## [13] -135.62103 -163.37447 -140.16612 -158.19439 -202.93001 -172.20640
## [19] -175.47633 -152.46025 -175.25008 -161.79431 -200.99433 -123.21707
## [25] -155.76501 -150.86815 -173.93209 -112.94435 -157.61162 -256.54004
## [31] -141.15356 -168.92073 -212.09429 -177.82023 -212.82667 -150.31654
## [37] -163.37063 -131.52089 -168.24690 -148.80640 -172.67586 -161.53184
## [43] -142.29569 -168.95538 -138.98197 -179.23861 -148.72280 -147.19814
## [49] -168.73177 -144.18682 -203.11569 -149.09933 -162.51061 -187.55448
## [55] -115.94868 -170.27951 -162.83568 -217.35582 -156.65085 -151.29802
## [61] -150.95600 -181.42498 -142.51989 -176.46663 -141.99558 -179.79159
## [67] -153.37136 -159.95511 -157.39933 -224.83147 -184.84833 -160.00933
## [73] -150.65233 -124.53687 -192.41115 -123.52518 -183.85366 -131.22570
## [79] -186.93345 -189.33652 -195.30783 -155.96404 -179.26647 -139.57985
## [85] -162.55241 -141.67257 -167.73387 -193.47192 -178.76800 -190.68335
## [91] -172.40508 -184.61498 -154.30964 -145.59120 -170.24623 -150.28391
## [97] -128.91751 -139.66003 -172.47869 -167.44124 -159.42051 -185.62485
## [103] -129.92302 -131.01888 -133.95496 -117.49642 -175.91396 -239.25715
## [109] -161.72833 -144.21519 -185.65161 -216.51232 -136.38307 -178.70724
## [115] -149.65483 -134.82366 -170.38692 -147.25478 -160.39573 -123.91204
## [121] -165.73064 -151.84122 -121.89093 -151.66496 -151.29975 -199.73648
## [127] -124.66442 -157.02835 -138.87554 -111.26449 -130.60238 -126.95121
## [133] -169.04520 -164.35731 -126.32743 -204.59389 -140.77325 -157.99992
## [139] -101.80260 -106.30295 -142.51099 -127.34227 -123.44447 -155.12642
## [145] -127.49479 -82.00206 -157.92806 -147.73823 -98.38925 -111.46555
## [151] -100.33344 -126.92388 -123.54508 -144.73988 -86.77186 -213.51775
## [157] -147.84391 -126.11083 -129.28461 -103.48483 -137.22447 -119.78358
## [163] -102.27284 -97.83168 -115.81180 -124.25095 -170.44873 -131.65819
## [169] -151.19680 -121.48943 -158.09647 -180.56485 -164.19484 -89.36727
## [175] -121.24537 -143.59805 -168.87761 -116.26350 -127.58339 -151.25376
## [181] -172.44480 -138.06864 -151.13447 -127.00970 -196.42395 -172.40085
## [187] -125.81790 -182.99695 -128.86183 -120.20819 -105.88243 -140.33888
## [193] -131.46182 -121.39904 -124.97155 -159.94777 -143.75144 -162.31866
## [199] -127.89970 -172.71214 -153.71183 -89.36742 -136.87713 -174.88072
## [205] -130.36593 -146.07916 -132.26158 -143.82089 -160.88127 -149.01852
## [211] -136.83911 -142.80486 -156.35414 -111.98380 -145.09466 -130.67802
## [217] -133.88761 -130.22035 -168.57470 -124.99053 -138.04592 -164.32860
## [223] -136.30871 -89.36588 -115.48645 -139.46846 -133.88759 -128.91322
## [229] -189.42542 -125.01930 -148.61547 -133.95717 -112.26478 -153.61366
## [235] -131.14988 -107.43253 -129.14727 -125.24838 -136.39091 -117.41039
## [241] -147.34207 -147.63838 -135.42983 -142.00482 -108.45658 -143.75252
## [247] -181.63584 -110.12154 -174.42375 -125.95997 -128.10251 -139.43903
## [253] -116.89171 -165.21592 -118.25317 -143.44609 -128.29258 -130.65612
## [259] -183.87339 -128.64913 -139.75567 -112.83394 -169.97089 -170.16516
## [265] -121.77907 -134.63846 -137.88988 -152.27370 -144.87453 -124.54711
## [271] -100.20947 -126.99696 -145.68618 -151.52954 -130.63294 -142.66773
## [277] -153.11077 -124.40445 -138.65356 -168.55849 -124.43606 -127.53927
## [283] -117.28961 -126.97602 -127.55061 -95.53446 -192.72696 -147.59125
## [289] -146.20695 -142.62357 -147.13648 -133.90095 -135.02596 -122.24356
## [295] -141.00084 -147.95654 -133.43449 -143.44252 -132.73279 -125.41423
## [301] -148.70928 -188.01832 -128.27511 -131.66379 -95.62613 -133.25751
## [307] -127.58233 -110.51969 -154.50552 -106.51430 -124.15500 -146.72284
## [313] -172.64585 -143.67139 -102.73025 -122.71984 -86.84573 -157.73652
## [319] -153.36982 -116.43881 -146.67815 -125.55154 -169.85471 -121.64719
## [325] -138.06466 -151.61127 -160.50146 -166.75131 -125.50644 -147.12736
## [331] -147.30392 -148.78479 -104.50398 -134.71764 -130.72686 -146.55922
## [337] -130.87232 -136.18069 -107.83464 -167.57867 -124.59558 -143.17446
## [343] -140.24678 -129.29453 -162.89874 -166.28248 -146.66690 -162.67599
## [349] -160.05653 -146.44655 -155.43767 -127.52049 -118.67063 -153.50561
## [355] -157.49454 -177.48818 -93.85254 -168.60288 -134.51250 -110.25318
## [361] -138.70366 -128.25050 -155.62744 -107.85156 -135.72983 -107.88442
## [367] -159.27492 -145.50379 -121.63035 -143.66191 -124.83032 -124.20623
## [373] -130.18657 -127.71988 -180.20086 -153.72427 -154.48370 -177.63914
## [379] -138.55687 -141.88591 -171.60176 -152.09452 -236.83146 -178.43746
## [385] -142.18885 -108.45688 -156.80361 -121.63702 -149.44715 -156.14226
## [391] -162.33880 -152.07215 -178.12631 -183.00801 -157.59487 -134.77876
## [397] -156.34734 -121.77048 -145.23555 -142.00196 -106.51670 -148.72672
## [403] -155.97134 -145.21833 -156.23124 -137.72854 -185.99113 -128.69370
## [409] -147.74050 -144.34907 -124.82191 -129.36980 -147.47991 -136.95383
## [415] -163.94135 -137.62349 -125.04795 -137.09875 -138.86232 -129.70749
## [421] -164.52603 -139.50320 -136.22981 -153.48004 -157.41817 -143.42072
## [427] -138.90364 -158.76978 -140.37750 -120.96811 -140.76238 -130.40090
## [433] -153.84070 -156.62087 -155.60210 -164.78571 -169.34215 -166.31287
## [439] -164.01010 -144.23136 -131.98623 -103.36942 -142.97916 -163.19553
## [445] -130.88623 -123.63384 -118.18769 -146.17333 -114.64744 -170.06602
## [451] -114.33881 -131.64419 -139.47960 -147.73918 -174.10566 -104.53887
## [457] -114.17888 -111.10554 -118.45082 -137.00545 -188.62105 -167.76275
## [463] -142.29261 -153.65623 -163.58208 -152.58976 -184.80046 -157.66594
## [469] -181.58812 -116.72893 -178.80781 -181.01732 -164.85902 -143.79504
## [475] -188.91725 -148.88208 -140.02662 -143.43035 -221.50114 -164.50821
## [481] -132.39106 -143.57809 -163.58215 -141.21097 -121.34421 -164.64414
## [487] -137.95950 -106.44765 -179.69714 -193.46573 -190.41538 -173.95245
## [493] -145.76543 -179.35816 -157.52029 -136.31303 -183.53033 -122.70149
## [499] -102.14471 -157.29261 -209.95777 -177.60153 -139.07573 -165.75548
## [505] -127.69367 -154.47418 -152.68377 -161.84158 -159.80496 -117.73050
## [511] -161.19559 -108.45486 -181.29137 -139.83049 -200.01687 -151.01596
## [517] -110.28999 -166.62874 -134.21145 -128.97768 -156.93635 -104.66972
## [523] -148.53171 -119.17531 -147.57400 -150.13537 -115.21348 -144.60942
## [529] -117.43348 -144.32068 -143.77389 -168.13531 -150.14340 -131.71507
## [535] -171.32550 -103.63711 -171.98976 -133.12754 -119.01253 -143.54389
## [541] -187.95568 -87.96063 -169.48712 -146.63552 -136.86964 -179.72952
## [547] -156.81142 -100.27911 -129.04133 -198.90118 -173.77336 -129.09094
## [553] -120.96139 -173.31704 -136.80484 -118.62337 -154.05099 -188.52093
## [559] -181.73756 -139.70905 -164.94759 -152.72598 -159.57798 -151.56299
## [565] -130.10781 -149.10992 -117.71425 -148.77855 -152.83822 -164.99411
## [571] -94.14491 -188.56834 -141.07980 -146.36482 -126.50648 -112.69998
## [577] -250.53381 -155.73922 -107.77877 -130.36916 -154.86298 -102.78153
## [583] -141.71601 -106.14463 -154.43294 -180.56530 -157.36571 -178.31661
## [589] -124.47376 -137.29236 -120.97155 -117.48997 -147.32941 -152.92664
## [595] -174.74145 -111.28768 -139.64491 -134.37641 -152.52284 -147.47157
## [601] -209.33629 -161.29622 -135.10839 -133.84927 -167.78807 -84.14179
## [607] -83.17912 -137.66894 -175.16146 -171.63735 -97.34890 -130.48960
## [613] -98.83927 -89.36286 -116.00517 -151.73756 -125.82888 -144.63080
## [619] -159.24469 -169.01434 -232.58785 -146.44855 -116.39453 -117.31219
## [625] -96.89372 -142.58999 -103.75609 -157.61342 -113.11446 -234.75761
## [631] -108.89545 -169.14536 -125.78257 -146.36486 -99.93656 -147.85557
## [637] -165.75978 -173.50993 -144.02554 -128.73179 -148.89146 -92.99652
## [643] -193.42957 -151.45846 -132.19101 -127.18005 -109.89029 -111.05164
## [649] -150.28971 -91.13359 -83.17809 -159.62035 -100.36764 -115.26042
## [655] -142.82495 -211.55654 -130.44872 -117.43755 -83.17809 -98.28055
## [661] -83.17798 -155.39450 -89.36254 -102.26821 -109.27461 -83.17796
## [667] -98.33297 -133.20551 -106.15431 -102.19438 -76.22737 -82.96148
## [673] -108.42216 -111.92532 -83.17795 -98.28032 -99.67164 -94.07488
## [679] -112.88846 -121.59238 -71.71728 -119.57328 -75.35691 -125.69652
## [685] -140.12968 -182.42863 -105.93781 -82.14881 -96.54908 -70.02801
## [691] -70.15221 -112.79825 -153.36947 -104.07403 -105.10979 -124.26705
## [697] -119.20712 -160.31436 -183.67867 -77.02873 -268.72525 -160.65366
## [703] -136.59695 -146.46778 -99.51414 -106.14711 -105.43009 -189.80694
## [709] -183.12629 -138.18745 -168.50406 -130.61056 -132.57538 -129.79341
## [715] -157.76729 -116.68900 -102.07545 -154.67828 -168.96051 -83.17771
## [721] -162.34480 -112.82872 -93.37081 -202.88086 -134.35108 -107.64814
## [727] -89.34529 -102.19832 -106.78771 -112.48178 -95.50744 -109.42504
## [733] -83.17766 -114.27190 -99.72779 -89.36224 -94.10938 -92.98278
## [739] -79.59264 -83.17766 -141.81174 -171.94322 -140.57629 -135.49077
## [745] -168.76135 -106.58271 -141.76777 -109.42025 -136.50161 -159.11353
## [751] -151.82580 -162.38541 -138.65777 -144.76380 -143.97385 -125.99820
## [757] -190.99845 -109.10167 -151.77143 -138.34984 -185.01880 -99.03314
## [763] -163.83989 -228.63306 -142.38450 -153.49910 -136.27776 -154.47385
## [769] -178.61999 -182.25483 -124.20855 -148.38150 -139.78625 -108.99424
## [775] -145.30026 -111.07351 -155.13460 -99.37286 -148.01411 -116.92223
## [781] -172.11203 -78.95382 -119.33265 -185.49359 -82.13128 -146.35223
## [787] -86.13955 -91.64367 -110.75443 -125.94889 -115.47015 -150.80358
## [793] -175.59500 -168.59771 -147.83881 -110.32290 -193.11392 -199.10892
## [799] -148.72740 -121.49148 -104.49041 -179.86984 -163.30736 -143.82735
## [805] -166.38900 -137.85028 -123.57950 -159.32759 -172.99989 -109.31211
## [811] -131.13846 -124.20073 -157.57556 -163.72814 -203.48019 -207.36210
## [817] -208.00003 -160.27366 -141.65906 -164.81244 -111.63093 -133.55027
## [823] -117.21334 -186.14577 -141.71738 -189.85324 -151.97157 -150.96083
## [829] -103.63781 -155.70894 -133.82138 -145.19459 -152.84574 -162.16555
## [835] -201.95717 -136.86360 -199.49306 -162.15737 -146.76264 -186.34161
## [841] -173.37082 -161.76230 -141.43346 -186.56137 -193.33006 -139.92860
## [847] -152.28339 -166.67350 -165.69485 -157.98113 -190.91277 -187.92296
## [853] -143.47574 -126.96078 -198.33234 -144.26319 -142.48095 -245.12697
## [859] -153.86214 -155.05570 -156.39458 -207.24505 -155.64650 -143.68310
## [865] -187.73614 -147.15878 -173.62912 -102.99032 -194.43794 -182.32089
## [871] -178.57826 -193.69341 -136.48060 -138.36565 -130.10479 -198.81169
## [877] -136.70451 -132.25203 -180.47351 -192.94054 -136.44712 -126.39597
## [883] -146.81479 -178.75733 -151.69628 -163.28627 -190.36830 -165.00978
## [889] -178.18600 -128.65037 -148.32343 -96.84980 -149.22297 -145.90827
## [895] -184.78905 -204.12277 -140.20038 -198.55054 -162.52896 -153.93190
## [901] -217.36124 -153.05562 -145.21919 -155.55851 -156.08003 -147.70770
## [907] -180.99750 -166.15077 -134.00465 -135.61337 -137.89550 -149.65987
## [913] -141.42883 -142.22890 -118.81791 -185.20248 -139.33345 -138.79771
## [919] -145.59510 -141.58859 -189.38833 -158.56551 -221.37953 -138.99897
## [925] -162.55169 -171.84905 -143.36994 -110.60287 -143.14426 -145.09781
## [931] -177.93949 -172.83917 -130.66396 -174.54722 -159.29762 -131.64282
## [937] -159.48450 -136.35646 -154.47537 -199.23481 -168.65103 -171.99653
## [943] -149.04639 -171.85454 -158.44797 -197.73159 -120.02845 -152.64328
## [949] -147.83617 -170.91633 -109.96986 -154.71008 -253.74572 -138.47937
## [955] -166.26047 -209.56708 -175.36566 -210.37811 -147.87809 -160.93753
## [961] -129.09948 -165.88834 -146.51917 -170.52717 -159.38848 -140.20321
## [967] -166.91877 -136.94558 -177.23336 -146.75682 -145.24619 -166.87763
## [973] -142.38834 -201.32898 -147.35109 -160.76699 -185.81472 -114.22519
## [979] -168.56080 -161.16375 -215.70825 -155.10080 -149.74876 -149.43978
## [985] -179.91110 -141.03738 -174.99201 -140.58730 -178.40205 -152.03371
## [991] -158.63940 -156.12667 -223.58685 -183.69789 -158.89840 -149.54850
## [997] -123.49149 -191.37232 -122.48997 -182.83295 -130.21174 -185.96388
## [1003] -188.37485 -194.36713 -155.03571 -178.37760 -138.72893 -161.71834
## [1009] -140.84366 -167.01131 -192.80867 -178.11246 -190.04617 -171.76847
## [1015] -184.02678 -153.74171 -145.03507 -169.73448 -149.83997 -128.50141
## [1021] -139.28797 -172.16719 -167.13256 -159.12214 -185.32717 -129.63979
## [1027] -130.73582 -133.68920 -117.28102 -175.73222 -239.08056 -161.60881
## [1033] -144.10570 -185.57234 -216.48606 -136.37104 -178.70042 -149.64944
## [1039] -134.81893 -170.38367 -147.25167 -160.39292 -123.91029 -165.72907
## [1045] -151.83971 -121.88984 -151.66405 -151.29886 -199.73575 -124.66369
## [1051] -157.02794 -138.87515 -111.26411 -130.60202 -126.95085 -169.04484
## [1057] -164.35696 -126.32707 -204.59355 -140.77291 -157.99958 -101.80226
## [1063] -106.30261 -142.51065 -127.34194 -123.44414 -155.12610 -127.49446
## [1069] -82.00174 -157.92774 -147.73792 -98.38893 -111.46524 -100.33313
## [1075] -126.92357 -123.54477 -144.73957 -86.77155 -213.51745 -147.84361
## [1081] -126.11053 -129.28431 -103.48453 -137.22417 -119.78329 -102.27255
## [1087] -97.83139 -115.81151 -124.25066 -170.44844 -131.65791 -151.19651
## [1093] -121.48915 -158.09619 -180.56456 -164.19456 -89.36699 -121.24508
## [1099] -143.59777 -168.87733 -116.26322 -127.58311 -151.25348 -172.44452
## [1105] -138.06836 -151.13419 -127.00942 -196.42367 -172.40058 -125.81762
## [1111] -182.99667 -128.86156 -120.20792 -105.88216 -140.33861 -131.46155
## [1117] -121.39877 -124.97128 -159.94750 -143.75117 -162.31839 -127.89944
## [1123] -172.71188 -153.71157 -89.36715 -136.87687 -174.88046 -130.36567
## [1129] -146.07890 -132.26132 -143.82064 -160.88102 -149.01827 -136.83886
## [1135] -142.80460 -156.35389 -111.98355 -145.09441 -130.67777 -133.88737
## [1141] -130.22010 -168.57446 -124.99028 -138.04567 -164.32835 -136.30846
## [1147] -89.36564 -115.48620 -139.46821 -133.88735 -128.91298 -189.42518
## [1153] -125.01906 -148.61522 -133.95693 -112.26454 -153.61342 -131.14964
## [1159] -107.43229 -129.14703 -125.24814 -136.39067 -117.41015 -147.34183
## [1165] -147.63814 -135.42960 -142.00459 -108.45635 -143.75229 -181.63561
## [1171] -110.12131 -174.42352 -125.95974 -128.10228 -139.43880 -116.89149
## [1177] -165.21569 -118.25294 -143.44587 -128.29235 -130.65589 -183.87317
## [1183] -128.64891 -139.75545 -112.83372 -169.97066 -170.16494 -121.77885
## [1189] -134.63824 -137.88965 -152.27348 -144.87431 -124.54689 -100.20925
## [1195] -126.99674 -145.68597 -151.52932 -130.63272 -142.66752 -153.11055
## [1201] -124.40423 -138.65335 -168.55828 -124.43584 -127.53906 -117.28940
## [1207] -126.97581 -127.55040 -95.53425 -192.72675 -147.59105 -146.20674
## [1213] -142.62337 -147.13627 -133.90074 -135.02576 -122.24335 -141.00064
## [1219] -147.95633 -133.43429 -143.44231 -132.73258 -125.41402 -148.70908
## [1225] -188.01811 -128.27491 -131.66358 -95.62593 -133.25731 -127.58213
## [1231] -110.51948 -154.50531 -106.51410 -124.15480 -146.72265 -172.64565
## [1237] -143.67120 -102.73006 -122.71964 -86.84554 -157.73632 -153.36962
## [1243] -116.43861 -146.67795 -125.55134 -169.85452 -121.64700 -138.06447
## [1249] -151.61108 -160.50127 -166.75112 -125.50625 -147.12717 -147.30373
## [1255] -148.78460 -104.50379 -134.71745 -130.72667 -146.55903 -130.87214
## [1261] -136.18050 -107.83445 -167.57848 -124.59539 -143.17428 -140.24660
## [1267] -129.29434 -162.89856 -166.28230 -146.66671 -162.67581 -160.05634
## [1273] -146.44637 -155.43749 -127.52031 -118.67045 -153.50543 -157.49436
## [1279] -177.48800 -93.85236 -168.60271 -134.51232 -110.25300 -138.70348
## [1285] -128.25033 -155.62727 -107.85138 -135.72965 -107.88425 -159.27474
## [1291] -145.50361 -121.63018 -143.66174 -124.83015 -124.20605 -130.18640
## [1297] -127.71970 -180.20069 -153.72410 -154.48352 -177.63897 -138.55670
## [1303] -141.88574 -171.60159 -152.09435 -236.83129 -178.43730 -142.18868
## [1309] -108.45671 -156.80344 -121.63686 -149.44698 -156.14210 -162.33864
## [1315] -152.07198 -178.12615 -183.00785 -157.59470 -134.77860 -156.34717
## [1321] -121.77032 -145.23538 -142.00180 -106.51654 -148.72656 -155.97118
## [1327] -145.21817 -156.23108 -137.72838 -185.99097 -128.69354 -147.74034
## [1333] -144.34891 -124.82175 -129.36965 -147.47975 -136.95368 -163.94119
## [1339] -137.62333 -125.04779 -137.09859 -138.86217 -129.70733 -164.52587
## [1345] -139.50305 -136.22965 -153.47988 -157.41802 -143.42057 -138.90349
## [1351] -158.76963 -140.37735 -120.96796 -140.76223 -130.40075 -153.84055
## [1357] -156.62072 -155.60195 -164.78556 -169.34200 -166.31272 -164.00995
## [1363] -144.23122 -131.98608 -103.36928 -142.97902 -163.19539 -130.88608
## [1369] -123.63370 -118.18755 -146.17319 -114.64730 -170.06588 -114.33867
## [1375] -131.64405 -139.47946 -147.73904 -174.10552 -104.53873 -114.17875
## [1381] -111.10540 -118.45068 -137.00532 -188.62092 -167.76262 -142.29247
## [1387] -153.65610 -163.58194 -152.58962 -184.80033 -157.66581 -181.58798
## [1393] -116.72879 -178.80768 -181.01719 -164.85889 -143.79491 -188.91712
## [1399] -148.88194 -140.02648 -143.43022 -221.50101 -164.50808 -132.39093
## [1405] -143.57796 -163.58202 -141.21084 -121.34409 -164.64401 -137.95937
## [1411] -106.44752 -179.69701 -193.46560 -190.41526 -173.95233 -145.76530
## [1417] -179.35804 -157.52016 -136.31291 -183.53020 -122.70137 -102.14459
## [1423] -157.29249 -209.95765 -177.60141 -139.07561 -165.75536 -127.69355
## [1429] -154.47406 -152.68365 -161.84146 -159.80485 -117.73038 -161.19548
## [1435] -108.45475 -181.29126 -139.83038 -200.01675 -151.01585 -110.28987
## [1441] -166.62863 -134.21134 -128.97756 -156.93624 -104.66961 -148.53160
## [1447] -119.17520 -147.57389 -150.13526 -115.21337 -144.60932 -117.43337
## [1453] -144.32057 -143.77379 -168.13521 -150.14330 -131.71497 -171.32539
## [1459] -103.63701 -171.98966 -133.12744 -119.01242 -143.54379 -187.95558
## [1465] -87.96053 -169.48702 -146.63542 -136.86954 -179.72942 -156.81133
## [1471] -100.27901 -129.04123 -198.90108 -173.77327 -129.09085 -120.96130
## [1477] -173.31694 -136.80475 -118.62328 -154.05090 -188.52084 -181.73747
## [1483] -139.70896 -164.94750 -152.72589 -159.57789 -151.56291 -130.10772
## [1489] -149.10984 -117.71417 -148.77846 -152.83813 -164.99403 -94.14483
## [1495] -188.56826 -141.07972 -146.36474 -126.50641 -112.69990 -250.53374
## [1501] -155.73914 -107.77870 -130.36908 -154.86290 -102.78146 -141.71594
## [1507] -106.14456 -154.43287 -180.56523 -157.36564 -178.31654 -124.47369
## [1513] -137.29229 -120.97148 -117.48990 -147.32935 -152.92658 -174.74138
## [1519] -111.28762 -139.64485 -134.37635 -152.52278 -147.47151 -209.33624
## [1525] -161.29616 -135.10834 -133.84922 -167.78802 -84.14173 -83.17906
## [1531] -137.66888 -175.16140 -171.63729 -97.34885 -130.48955 -98.83922
## [1537] -89.36281 -116.00512 -151.73751 -125.82883 -144.63076 -159.24464
## [1543] -169.01429 -232.58780 -146.44850 -116.39449 -117.31214 -96.89368
## [1549] -142.58995 -103.75604 -157.61337 -113.11442 -234.75756 -108.89541
## [1555] -169.14532 -125.78252 -146.36482 -99.93652 -147.85552 -165.75974
## [1561] -173.50989 -144.02550 -128.73175 -148.89142 -92.99648 -193.42954
## [1567] -151.45842 -132.19097 -127.18001 -109.89025 -111.05161 -150.28967
## [1573] -91.13355 -83.17805 -159.62032 -100.36760 -115.26038 -142.82491
## [1579] -211.55651 -130.44869 -117.43752 -83.17806 -98.28052 -83.17795
## [1585] -155.39447 -89.36251 -102.26818 -109.27458 -83.17793 -98.33294
## [1591] -133.20548 -106.15428 -102.19435 -76.22735 -82.96145 -108.42213
## [1597] -111.92529 -83.17792 -98.28029 -99.67162 -94.07485 -112.88843
## [1603] -121.59235 -71.71725 -119.57325 -75.35688 -125.69650 -140.12965
## [1609] -182.42860 -105.93778 -82.14879 -96.54906 -70.02798 -70.15218
## [1615] -112.79823 -153.36945 -104.07400 -105.10976 -124.26703 -119.20709
## [1621] -160.31434 -183.67865 -77.02871 -268.72523 -160.65364 -136.59694
## [1627] -146.46776 -99.51412 -106.14709 -105.43007 -189.80692 -183.12627
## [1633] -138.18744 -168.50405 -130.61054 -132.57537 -129.79339 -157.76728
## [1639] -116.68899 -102.07544 -154.67827 -168.96050 -83.17771 -162.34479
## [1645] -112.82871 -93.37081 -202.88086 -134.35108 -107.64813 -89.34529
## [1651] -102.19832 -106.78771 -112.48178 -95.50744 -109.42504 -83.17766
## [1657] -114.27190 -99.72779 -89.36224 -94.10938 -92.98278 -79.59264
## [1663] -83.17766 -141.81174 -171.94322 -140.57629 -135.49077 -168.76136
## [1669] -106.58272 -141.76778 -109.42026 -136.50162 -159.11355 -151.82582
## [1675] -162.38543 -138.65778 -144.76383 -143.97388 -125.99823 -190.99848
## [1681] -109.10170 -151.77147 -138.34988 -185.01884 -99.03318 -163.83994
## [1687] -228.63311 -142.38456 -153.49916 -136.27782 -154.47392 -178.62006
## [1693] -182.25490 -124.20863 -148.38158 -139.78633 -108.99433 -145.30035
## [1699] -111.07360 -155.13469 -99.37296 -148.01422 -116.92234 -172.11214
## [1705] -78.95394 -119.33278 -185.49371 -82.13141 -146.35236 -86.13968
## [1711] -91.64381 -110.75458 -125.94905 -115.47031 -150.80379 -175.59524
## [1717] -168.59795 -147.83906 -110.32319 -193.11423 -199.10923 -148.72772
## [1723] -121.49185 -104.49088 -179.87031 -163.30790 -143.82803 -166.38968
## [1729] -137.85107 -123.58034 -159.32850 -173.00097 -109.31320 -131.13956
## [1735] -124.20189 -157.57997 -163.73512 -203.49115 -207.37664 -208.04451
## [1741] -160.32592 -141.71213 -164.86642 -111.70318 -133.63971 -117.30289
## [1747] -186.27064 -141.86976 -190.03703 -152.15714 -151.16210 -103.86719
## [1753] -155.94605 -134.07798 -145.46075 -153.11320 -162.44873 -202.37852
## [1759] -137.31386 -200.03058 -162.71633 -147.32692 -186.96133 -174.00145
## [1765] -162.41155 -142.12229 -187.25215 -194.07566 -140.68562 -153.10266
## [1771] -167.56494 -166.67260 -158.99657 -191.95742 -189.02607 -144.60651
## [1777] -128.11948 -199.52866 -145.47103 -143.72807 -246.49717 -155.24926
## [1783] -156.48663 -157.86743 -208.74204 -157.17538 -145.23077 -189.33932
## [1789] -148.88939 -175.41771 -104.79697 -196.24937 -184.16379 -180.46726
## [1795] -195.61888 -138.44623 -140.33579 -132.09184 -200.80727 -138.74314
## [1801] -134.30100 -182.54989 -195.06775 -138.63952 -128.61030 -149.04854
## [1807] -181.00065 -153.94497 -165.53666 -192.65067 -167.37585 -180.64974
## [1813] -131.19877 -150.92230 -99.48954 -151.87143 -148.60426 -187.49550
## [1819] -206.84643 -142.93540 -201.30612 -165.32570 -156.78327 -220.21644
## [1825] -155.98396 -148.16298 -158.58552 -159.13583 -150.89417 -184.18785
## [1831] -169.43696 -137.36542 -138.98110 -141.26632 -153.58779 -145.39444
## [1837] -146.29570 -123.05816 -189.44314 -144.08010 -143.57884 -150.92808
## [1843] -146.92587 -196.33718 -165.76910 -230.48950library(dplyr)
select(likelihoods, Petalura_out, Phenes_out, Petalura_vs_Phenes)## Petalura_out Phenes_out Petalura_vs_Phenes
## 463 -146.20874 -138.99897 -7.20977520
## 750 -169.44146 -162.55169 -6.88976290
## 685 -177.71388 -171.84905 -5.86482490
## 286 -148.81612 -143.36994 -5.44617530
## 274 -115.50141 -110.60287 -4.89854010
## 318 -147.98243 -143.14426 -4.83816210
## 831 -149.72151 -145.09781 -4.62369780
## 738 -182.24006 -177.93949 -4.30056850
## 898 -176.96057 -172.83917 -4.12139750
## 714 -134.76466 -130.66396 -4.10069950
## 465 -178.60696 -174.54722 -4.05973970
## 686 -163.29787 -159.29762 -4.00024490
## 716 -135.62103 -131.64282 -3.97821270
## 135 -163.37447 -159.48450 -3.88996920
## 299 -140.16612 -136.35646 -3.80966570
## 920 -158.19439 -154.47537 -3.71902090
## 355 -202.93001 -199.23481 -3.69519880
## 730 -172.20640 -168.65103 -3.55537650
## 631 -175.47633 -171.99653 -3.47980590
## 29 -152.46025 -149.04639 -3.41386390
## 786 -175.25008 -171.85454 -3.39553150
## 430 -161.79431 -158.44797 -3.34634020
## 485 -200.99433 -197.73159 -3.26274210
## 582 -123.21707 -120.02845 -3.18861220
## 834 -155.76501 -152.64328 -3.12173150
## 596 -150.86815 -147.83617 -3.03197830
## 266 -173.93209 -170.91633 -3.01575420
## 826 -112.94435 -109.96986 -2.97449420
## 147 -157.61162 -154.71008 -2.90153120
## 459 -256.54004 -253.74572 -2.79431760
## 194 -141.15356 -138.47937 -2.67419370
## 27 -168.92073 -166.26047 -2.66025650
## 544 -212.09429 -209.56708 -2.52721080
## 881 -177.82023 -175.36566 -2.45457660
## 545 -212.82667 -210.37811 -2.44856640
## 444 -150.31654 -147.87809 -2.43845760
## 652 -163.37063 -160.93753 -2.43310260
## 290 -131.52089 -129.09948 -2.42141510
## 451 -168.24690 -165.88834 -2.35856270
## 573 -148.80640 -146.51917 -2.28723680
## 161 -172.67586 -170.52717 -2.14869440
## 676 -161.53184 -159.38848 -2.14336130
## 900 -142.29569 -140.20321 -2.09248280
## 263 -168.95538 -166.91877 -2.03661160
## 150 -138.98197 -136.94558 -2.03638920
## 754 -179.23861 -177.23336 -2.00525730
## 868 -148.72280 -146.75682 -1.96598080
## 547 -147.19814 -145.24619 -1.95195140
## 883 -168.73177 -166.87763 -1.85414290
## 739 -144.18682 -142.38834 -1.79848990
## 675 -203.11569 -201.32898 -1.78671420
## 462 -149.09933 -147.35109 -1.74824640
## 289 -162.51061 -160.76699 -1.74361680
## 65 -187.55448 -185.81472 -1.73975890
## 890 -115.94868 -114.22519 -1.72349070
## 452 -170.27951 -168.56080 -1.71871350
## 254 -162.83568 -161.16375 -1.67192830
## 740 -217.35582 -215.70825 -1.64757060
## 466 -156.65085 -155.10080 -1.55005310
## 220 -151.29802 -149.74876 -1.54926510
## 460 -150.95600 -149.43978 -1.51622210
## 654 -181.42498 -179.91110 -1.51387550
## 727 -142.51989 -141.03738 -1.48250870
## 622 -176.46663 -174.99201 -1.47462630
## 680 -141.99558 -140.58730 -1.40828240
## 824 -179.79159 -178.40205 -1.38954200
## 838 -153.37136 -152.03371 -1.33764880
## 218 -159.95511 -158.63940 -1.31570880
## 359 -157.39933 -156.12667 -1.27265910
## 923 -224.83147 -223.58685 -1.24461900
## 715 -184.84833 -183.69789 -1.15044260
## 181 -160.00933 -158.89840 -1.11093050
## 848 -150.65233 -149.54850 -1.10382390
## 709 -124.53687 -123.49149 -1.04538570
## 271 -192.41115 -191.37232 -1.03882950
## 583 -123.52518 -122.48997 -1.03520540
## 649 -183.85366 -182.83295 -1.02071590
## 778 -131.22570 -130.21174 -1.01395760
## 251 -186.93345 -185.96388 -0.96956590
## 11 -189.33652 -188.37485 -0.96167250
## 567 -195.30783 -194.36713 -0.94069330
## 40 -155.96404 -155.03571 -0.92833440
## 252 -179.26647 -178.37760 -0.88887170
## 777 -139.57985 -138.72893 -0.85091450
## 850 -162.55241 -161.71834 -0.83406490
## 771 -141.67257 -140.84366 -0.82891880
## 860 -167.73387 -167.01131 -0.72255500
## 556 -193.47192 -192.80867 -0.66325130
## 817 -178.76800 -178.11246 -0.65553650
## 117 -190.68335 -190.04617 -0.63718010
## 384 -172.40508 -171.76847 -0.63660920
## 918 -184.61498 -184.02678 -0.58820410
## 325 -154.30964 -153.74171 -0.56793340
## 726 -145.59120 -145.03507 -0.55612600
## 91 -170.24623 -169.73448 -0.51175390
## 683 -150.28391 -149.83997 -0.44393640
## 506 -128.91751 -128.50141 -0.41610130
## 262 -139.66003 -139.28797 -0.37206720
## 722 -172.47869 -172.16719 -0.31150120
## 329 -167.44124 -167.13256 -0.30867950
## 585 -159.42051 -159.12214 -0.29837310
## 613 -185.62485 -185.32717 -0.29768390
## 235 -129.92302 -129.63979 -0.28322950
## 662 -131.01888 -130.73582 -0.28305790
## 894 -133.95496 -133.68920 -0.26576510
## 305 -117.49642 -117.28102 -0.21540110
## 827 -175.91396 -175.73222 -0.18174560
## 623 -239.25715 -239.08056 -0.17659830
## 154 -161.72833 -161.60881 -0.11952390
## 2 -144.21519 -144.10570 -0.10949060
## 196 -185.65161 -185.57234 -0.07927230
## 323 -216.51232 -216.48606 -0.02626250
## 291 -136.38307 -136.37104 -0.01202500
## 171 -178.70724 -178.70042 -0.00681710
## 182 -149.65483 -149.64944 -0.00538970
## 720 -134.82366 -134.81893 -0.00473160
## 321 -170.38692 -170.38367 -0.00324970
## 885 -147.25478 -147.25167 -0.00310380
## 158 -160.39573 -160.39292 -0.00280470
## 264 -123.91204 -123.91029 -0.00175210
## 643 -165.73064 -165.72907 -0.00157050
## 123 -151.84122 -151.83971 -0.00150680
## 272 -121.89093 -121.88984 -0.00108350
## 512 -151.66496 -151.66405 -0.00091300
## 767 -151.29975 -151.29886 -0.00088580
## 659 -199.73648 -199.73575 -0.00073080
## 820 -124.66442 -124.66369 -0.00072940
## 392 -157.02835 -157.02794 -0.00040620
## 869 -138.87554 -138.87515 -0.00038140
## 536 -111.26449 -111.26411 -0.00037680
## 129 -130.60238 -130.60202 -0.00036520
## 15 -126.95121 -126.95085 -0.00036410
## 415 -169.04520 -169.04484 -0.00035690
## 20 -164.35731 -164.35696 -0.00035250
## 624 -126.32743 -126.32707 -0.00035230
## 472 -204.59389 -204.59355 -0.00034230
## 641 -140.77325 -140.77291 -0.00034120
## 312 -157.99992 -157.99958 -0.00033930
## 441 -101.80260 -101.80226 -0.00033900
## 10 -106.30295 -106.30261 -0.00033890
## 697 -142.51099 -142.51065 -0.00033850
## 702 -127.34227 -127.34194 -0.00033130
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## 594 -221.37953 -230.48950 9.10997730likelihoods <- likelihoods[order(likelihoods$Phenes_vs_Uropetala),]
likelihoods$orders<-1:length(likelihoods$Phenes_vs_Uropetala)
likelihoods$col <- likelihoods$Phenes_out
for (x in 1:length(likelihoods$Phenes_out)) {
if(likelihoods$Phenes_vs_Uropetala[[x]] < 0){
likelihoods$col[x] <- "Uropetala"
}else if (likelihoods$Phenes_vs_Uropetala[[x]] > 0){
likelihoods$col[x] <- "Phenes"
}else{
likelihoods$col[x] <- "Relationships are\nequally likely"
}
}
ggplot(likelihoods, aes(x=orders, y=Phenes_vs_Uropetala, color = col)) + geom_point(size=2) + scale_color_brewer(palette="Dark2") + theme_minimal()+geom_hline(yintercept=0)+labs(y="Likelihood of Outgroup",x="") +
labs(title = "Supported Outgroup of Gondwanan Clade") + theme(plot.title = element_text(hjust = 0.5, face = "bold.italic", size = 20)) + labs(color = "Supported Outgroup") + theme(legend.text=element_text(size=12, face = "italic")) + theme(legend.title=element_text(size=15)) + guides(colour = guide_legend(override.aes = list(size=10))) + theme(text = element_text(family = "Times New Roman"))
library(stringr)
likelihoods <- likelihoods[order(likelihoods$ingentissima_vs_gigantea),]
likelihoods$orders<-1:length(likelihoods$ingentissima_vs_gigantea)
likelihoods$col <- likelihoods$ingentissima_out
for (x in 1:length(likelihoods$Petalura_out)) {
if(likelihoods$ingentissima_vs_gigantea[[x]] < 0){
likelihoods$col[x] <- "Sister to P. gigantea\nand P. litorea"
}else if (likelihoods$ingentissima_vs_gigantea[[x]] > 0){
likelihoods$col[x] <- "Sister to P. ingentissima"
}else{
likelihoods$col[x] <- "Relationships are\nequally likely"
}
}
ggplot(likelihoods, aes(x=orders, y=ingentissima_vs_gigantea, color = col)) +
geom_point(size=2) +
scale_color_brewer(palette="Dark2") + theme_minimal() +
geom_hline(yintercept=0) +labs(y="Likelihood of Relationship",x="") +
labs(title = "Supported placement of Petalura hesperia") +
theme(plot.title = element_text(hjust = 0.5, face = "bold.italic", size = 20)) +
labs(color = "Supported relationship") +
theme(legend.text=element_text(size=12, face = "italic")) + theme(legend.title=element_text(size=15)) +
theme(text = element_text(family = "Times New Roman")) +
guides(colour = guide_legend(override.aes = list(size=10))) 
likelihoods$ingentissima_vs_gigantea <- likelihoods$Phenes_out - likelihoods$hesperia_alternate
likelihoods$ingentissima_vs_out <- likelihoods$Phenes_out - likelihoods$hesperia_out
likelihoods$gigantea_vs_out <- likelihoods$hesperia_alternate - likelihoods$hesperia_out
likelihoods <- likelihoods[order(likelihoods$gigantea_vs_out),]
likelihoods$orders<-1:length(likelihoods$gigantea_vs_out)
likelihoods$col <- likelihoods$gigantea_out
for (x in 1:length(likelihoods$Petalura_out)) {
if(likelihoods$gigantea_vs_out[[x]] < 0){
likelihoods$col[x] <- "Sister to the rest\nof Petalura"
}else if (likelihoods$gigantea_vs_out[[x]] > 0){
likelihoods$col[x] <- "Sister to P. gigantea\nand P. litorea"
}else{
likelihoods$col[x] <- "Relationships are\nequally likely"
}
}
ggplot(likelihoods, aes(x=orders, y=gigantea_vs_out, color = col)) +
geom_point(size=2) +
scale_color_brewer(palette="Dark2") + theme_minimal() +
geom_hline(yintercept=0) +labs(y="Likelihood of Relationship",x="") +
labs(title = "Supported placement of Petalura hesperia") +
theme(plot.title = element_text(hjust = 0.5, face = "bold.italic", size = 20)) +
labs(color = "Supported relationship") +
theme(legend.text=element_text(size=12, face = "italic")) + theme(legend.title=element_text(size=15)) +
theme(text = element_text(family = "Times New Roman")) +
guides(colour = guide_legend(override.aes = list(size=10))) 
likelihoods$ingentissima_vs_gigantea <- likelihoods$Phenes_out - likelihoods$hesperia_alternate
likelihoods$ingentissima_vs_out <- likelihoods$Phenes_out - likelihoods$hesperia_out
likelihoods$gigantea_vs_out <- likelihoods$hesperia_alternate - likelihoods$hesperia_out
likelihoods <- likelihoods[order(likelihoods$ingentissima_vs_out),]
likelihoods$orders<-1:length(likelihoods$ingentissima_vs_out)
likelihoods$col <- likelihoods$ingentissima_out
for (x in 1:length(likelihoods$Petalura_out)) {
if(likelihoods$ingentissima_vs_out[[x]] < 0){
likelihoods$col[x] <- "Sister to the rest\nof Petalura"
}else if (likelihoods$ingentissima_vs_out[[x]] > 0){
likelihoods$col[x] <- "Sister to P. ingentissima"
}else{
likelihoods$col[x] <- "Relationships are\nequally likely"
}
}
ggplot(likelihoods, aes(x=orders, y=ingentissima_vs_out, color = col)) + geom_point(size=2) +
geom_point(size=2) +
scale_color_brewer(palette="Dark2") + theme_minimal() +
geom_hline(yintercept=0) +labs(y="Likelihood of Relationship",x="") +
labs(title = "Supported placement of Petalura hesperia") +
theme(plot.title = element_text(hjust = 0.5, face = "bold.italic", size = 20)) +
labs(color = "Supported relationship") +
theme(legend.text=element_text(size=12, face = "italic")) + theme(legend.title=element_text(size=15)) +
theme(text = element_text(family = "Times New Roman")) +
guides(colour = guide_legend(override.aes = list(size=10))) 
######Modeling support##############
library(dplyr)
library(RevGadgets)
library(coda)
library(grid)
library(gridExtra)
library(maps)
library(readr)
library(dplyr)
library(RColorBrewer)
library(stringr)
library(nnet)
library(tidyr)##
## Attaching package: 'tidyr'## The following object is masked from 'package:ggtree':
##
## expandlibrary(ggplot2)
likelihoods <- read.table("gene_likelihoods.tsv", head =T, sep="\t")calculate likelihoods and best option
likelihoods$Petalura_vs_Uropetala <- likelihoods$Petalura_out - likelihoods$Uropetala_out
likelihoods$Petalura_vs_Phenes <- likelihoods$Petalura_out - likelihoods$Phenes_out
likelihoods$Phenes_vs_Uropetala <- likelihoods$Phenes_out - likelihoods$Uropetala_out
likelihoods$ingentissima_vs_gigantea <- likelihoods$Phenes_out - likelihoods$hesperia_alternate
likelihoods$ingentissima_vs_out <- likelihoods$Phenes_out - likelihoods$hesperia_out
likelihoods$gigantea_vs_out <- likelihoods$hesperia_alternate - likelihoods$hesperia_out
likelihoods$best_relationship <- c()
for (x in 1:length(likelihoods$Petalura_out)) {
if(likelihoods$Petalura_out[[x]] > likelihoods$Phenes_out[[x]] & likelihoods$Petalura_out[[x]] > likelihoods$Uropetala_out[[x]]){
likelihoods$best_relationship[x] <- "Petalura"
}else if (likelihoods$Phenes_out[[x]] > likelihoods$Uropetala_out[[x]] &
likelihoods$Phenes_out[[x]] > likelihoods$Petalura_out[[x]]){
likelihoods$best_relationship[x] <- "Phenes"
}else if (likelihoods$Uropetala_out[[x]] > likelihoods$Phenes_out[[x]]
& likelihoods$Uropetala_out[[x]] > likelihoods$Petalura_out[[x]]){
likelihoods$best_relationship[x] <- "Uropetala"
}else{
likelihoods$best_relationship[x] <- "Unclear"
}
}
likelihoods$best_relationship_Petalura <- c()
for (x in 1:length(likelihoods$Petalura_out)) {
if(likelihoods$Phenes_out[[x]] > likelihoods$hesperia_out[[x]] & likelihoods$Phenes_out[[x]] > likelihoods$hesperia_alternate[[x]]){
likelihoods$best_relationship_Petalura[x] <- "ingentissima"
}else if (likelihoods$hesperia_alternate[[x]] > likelihoods$hesperia_out[[x]] &
likelihoods$hesperia_alternate[[x]] > likelihoods$Phenes_out[[x]]){
likelihoods$best_relationship_Petalura[x] <- "gigantea_litorea"
}else if (likelihoods$hesperia_out[[x]] > likelihoods$Phenes_out[[x]]
& likelihoods$hesperia_out[[x]] > likelihoods$hesperia_alternate[[x]]){
likelihoods$best_relationship_Petalura[x] <- "Sister"
}else{
likelihoods$best_relationship_Petalura[x] <- "Unclear"
}
}remove NA’s (any row with an NA is omitted from all analysis)
likelihoods <- na.omit(likelihoods)classify chromosomes
do not evaluate since not being used, but left for stephen’s reference
#summary(as.factor(likelihoods$best_relationship))
likelihoods$chromosome <- as.factor(likelihoods$chromosome)
likelihoods$chr_classification <- c()
for (x in 1:length(likelihoods$chromosome)) {
if(likelihoods$chromosome[[x]] == "chr_HiC_scaffold_9"){
likelihoods$chr_classification[x] <- "Sex"
}else if (likelihoods$chromosome[[x]] == "chr_HiC_scaffold_8"){
likelihoods$chr_classification[x] <- "Micro"
}else if (likelihoods$chromosome[[x]] == "not_recovered_in_genome"){
likelihoods$chr_classification[x] <- "not_recovered_in_genome"
}else if (likelihoods$chromosome[[x]] == "not_recovered_in_genome"){
likelihoods$chr_classification[x] <- "not_recovered_in_genome"
}
else{
likelihoods$chr_classification[x] <- "autosome"
}
}
likelihoods$chr_classification <- as.factor(likelihoods$chr_classification)save copy of of object for use in pie charts before we remove everything
likelihoods_pie <- likelihoodsgenus comparison
remove
- microchromosomes
- not clear relationships
- note in doing this we remove unclear relationships for the genus comparison for the petulura analysis too, even though that analysis doesn’t use chromosome location
- hesperia alternate column
- not sure why (doesn’t matter), so commented out removal below
#likelihoods <- likelihoods[,-1]
likelihoods$best_relationship <- as.factor(likelihoods$best_relationship)
likelihoods <- likelihoods %>%
dplyr::filter(chromosome != "chr_HiC_scaffold_8") %>%
dplyr::filter(chromosome != "not_recovered_in_genome") %>%
dplyr::filter(best_relationship != "Unclear")remove empty levels
likelihoods$chromosome <- factor(likelihoods$chromosome)
likelihoods$best_relationship <- factor(likelihoods$best_relationship)eda
what does this look like?
ggplot(likelihoods_pie, aes(y = mean_substitution_rate, x = chromosome, color=best_relationship)) +
geom_jitter(width = .5) +
facet_wrap(~chromosome, scales = "free")
# theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))pie charts
did you mix these up somewhere? you had this hand input…
summary(as.factor(likelihoods$best_relationship))## Petalura Phenes Uropetala
## 135 609 99data <- data.frame(
group=c("Phenes", "Petalura", "Uropetala", "Unclear"),
value=c(652,147,17,107)
)
# Basic piechart
ggplot(data, aes(x="", y=value, fill=group)) +
geom_bar(stat="identity", width=1) +
coord_polar("y", start=0) +
theme_void()
but i get this from earlier object
pie_data <- data.frame(table(likelihoods_pie$best_relationship))
pie_data## Var1 Freq
## 1 Petalura 147
## 2 Phenes 653
## 3 Unclear 15
## 4 Uropetala 108library(ggtext)
library(plyr)## ------------------------------------------------------------------------------## You have loaded plyr after dplyr - this is likely to cause problems.
## If you need functions from both plyr and dplyr, please load plyr first, then dplyr:
## library(plyr); library(dplyr)## ------------------------------------------------------------------------------##
## Attaching package: 'plyr'## The following objects are masked from 'package:dplyr':
##
## arrange, count, desc, failwith, id, mutate, rename, summarise,
## summarize## The following object is masked from 'package:maps':
##
## ozonepie_data$Group <- revalue(pie_data$Var1,
c("Petalura"= "*Petalura*",
"Phenes" = "*Phenes*",
"Uropetala"= "*Uropetala*"))
ggplot(pie_data, aes(x="", y=Freq, fill=Group)) +
geom_bar(stat="identity", width=1) +
coord_polar("y", start=0) +
theme_void()+
labs(fill="Clade placement support")+
theme(
legend.text = element_markdown(color = "black", size = 11)
)
or could do
ggplot(likelihoods_pie,aes(x=chromosome)) +
geom_bar(aes(fill=best_relationship), position = "fill")+
labs(x= "Chromosome",
y= "Proportion")+
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
analysis
lots of help @ https://stats.oarc.ucla.edu/r/dae/multinomial-logistic-regression/
set reference level
likelihoods$best_relationship <- relevel(likelihoods$best_relationship, ref = "Phenes")develop model
run model
#install.packages("afex")
library(afex)## Loading required package: lme4## Loading required package: Matrix##
## Attaching package: 'Matrix'## The following objects are masked from 'package:tidyr':
##
## expand, pack, unpack## The following object is masked from 'package:ggtree':
##
## expand## ************
## Welcome to afex. For support visit: http://afex.singmann.science/## - Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
## - Methods for calculating p-values with mixed(): 'S', 'KR', 'LRT', and 'PB'
## - 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests
## - Get and set global package options with: afex_options()
## - Set sum-to-zero contrasts globally: set_sum_contrasts()
## - For example analyses see: browseVignettes("afex")
## ************##
## Attaching package: 'afex'## The following object is masked from 'package:lme4':
##
## lmerset_sum_contrasts() # use sum coding, necessary to make type III LR tests valid## setting contr.sum globally: options(contrasts=c('contr.sum', 'contr.poly'))multinom_model_br <- multinom(best_relationship ~ chromosome*mean_substitution_rate , data = likelihoods)## # weights: 63 (40 variable)
## initial value 926.130159
## iter 10 value 638.977051
## iter 20 value 628.484069
## iter 30 value 626.836717
## iter 40 value 625.469571
## iter 50 value 624.644489
## iter 60 value 624.587339
## final value 624.587137
## convergedsummary(multinom_model_br)## Call:
## multinom(formula = best_relationship ~ chromosome * mean_substitution_rate,
## data = likelihoods)
##
## Coefficients:
## (Intercept) chromosome1 chromosome2 chromosome3 chromosome4
## Petalura -32.326449 31.7505106 31.5456613 30.7023248 31.1202065
## Uropetala -1.265085 -0.8856289 -0.3695525 -0.6697151 0.4271093
## chromosome5 chromosome6 chromosome7 chromosome8 chromosome9
## Petalura 30.4952023 31.027838 30.6797515 31.1760809 -279.9901355
## Uropetala 0.2264045 1.088448 -0.3664671 0.3528065 -0.6351915
## mean_substitution_rate chromosome1:mean_substitution_rate
## Petalura 7.2827096 -7.5674933
## Uropetala -0.3082528 0.4737669
## chromosome2:mean_substitution_rate chromosome3:mean_substitution_rate
## Petalura -7.491314 -7.3040001
## Uropetala 0.210613 0.5526143
## chromosome4:mean_substitution_rate chromosome5:mean_substitution_rate
## Petalura -7.1554830 -7.3571706
## Uropetala -0.1229367 -0.4384231
## chromosome6:mean_substitution_rate chromosome7:mean_substitution_rate
## Petalura -7.4414551 -7.3506975
## Uropetala -0.9893523 0.2317449
## chromosome8:mean_substitution_rate chromosome9:mean_substitution_rate
## Petalura -7.7675020 68.4596057
## Uropetala -0.1676495 0.2799027
##
## Std. Errors:
## (Intercept) chromosome1 chromosome2 chromosome3 chromosome4
## Petalura 2.6394380 2.6662322 2.6605309 2.7337564 2.6884138
## Uropetala 0.2412622 0.4891966 0.4834153 0.6750892 0.7510515
## chromosome5 chromosome6 chromosome7 chromosome8 chromosome9
## Petalura 2.6735533 2.6683129 2.6902129 2.7280968 23.628947
## Uropetala 0.6464245 0.7815506 0.5819758 0.6712675 1.156604
## mean_substitution_rate chromosome1:mean_substitution_rate
## Petalura 11.1900715 11.1917596
## Uropetala 0.1349919 0.1951348
## chromosome2:mean_substitution_rate chromosome3:mean_substitution_rate
## Petalura 11.1912300 11.1947264
## Uropetala 0.2254581 0.2739507
## chromosome4:mean_substitution_rate chromosome5:mean_substitution_rate
## Petalura 11.1924405 11.1916637
## Uropetala 0.4367927 0.4239558
## chromosome6:mean_substitution_rate chromosome7:mean_substitution_rate
## Petalura 11.1917349 11.1924308
## Uropetala 0.5624124 0.2704931
## chromosome8:mean_substitution_rate chromosome9:mean_substitution_rate
## Petalura 11.1968698 100.6887171
## Uropetala 0.3718238 0.6313904
##
## Residual Deviance: 1249.174
## AIC: 1329.174assumptions
linear relationship between predictor and modeled outcome (logit)
# Select only outcome and numeric predictors
# drop missing and save in new dataset
df_model <- likelihoods %>%
dplyr::select("mean_substitution_rate") %>% # enter numeric variables
drop_na(mean_substitution_rate) # drop cases with missing values on these variables.
# save names of predictors to plug into command below.
predictors <- colnames(df_model)
# Save predicted probabilities
df_model$probabilities <- multinom_model_br$fitted.values[,1]
# Manually calculate the logit values and tidy data for the plot
df_model <- df_model %>%
mutate(logit = log(probabilities/(1-probabilities))) %>%
dplyr::select(-probabilities) %>%
gather(key = "predictors", value = "predictor.value", -logit)
ggplot(df_model, aes(y = logit, x = predictor.value))+
geom_point(size = 0.5, alpha = 0.5) +
geom_smooth(method = "loess") +
theme_bw() +
facet_wrap(~predictors, scales = "free_x")## `geom_smooth()` using formula = 'y ~ x'
results
wald tests
z <- summary(multinom_model_br)$coefficients/summary(multinom_model_br)$standard.errors
z## (Intercept) chromosome1 chromosome2 chromosome3 chromosome4
## Petalura -12.247474 11.908382 11.8569046 11.2308194 11.5756759
## Uropetala -5.243609 -1.810374 -0.7644617 -0.9920394 0.5686818
## chromosome5 chromosome6 chromosome7 chromosome8 chromosome9
## Petalura 11.4062445 11.628261 11.4042095 11.4277768 -11.8494546
## Uropetala 0.3502412 1.392677 -0.6296947 0.5255826 -0.5491868
## mean_substitution_rate chromosome1:mean_substitution_rate
## Petalura 0.6508189 -0.6761665
## Uropetala -2.2834913 2.4278951
## chromosome2:mean_substitution_rate chromosome3:mean_substitution_rate
## Petalura -0.6693915 -0.6524501
## Uropetala 0.9341560 2.0172035
## chromosome4:mean_substitution_rate chromosome5:mean_substitution_rate
## Petalura -0.6393139 -0.6573795
## Uropetala -0.2814532 -1.0341247
## chromosome6:mean_substitution_rate chromosome7:mean_substitution_rate
## Petalura -0.6649063 -0.6567561
## Uropetala -1.7591225 0.8567496
## chromosome8:mean_substitution_rate chromosome9:mean_substitution_rate
## Petalura -0.6937208 0.6799134
## Uropetala -0.4508843 0.4433116p <- (1 - pnorm(abs(z), 0, 1)) * 2
p## (Intercept) chromosome1 chromosome2 chromosome3 chromosome4
## Petalura 0.000000e+00 0.00000000 0.0000000 0.0000000 0.0000000
## Uropetala 1.574657e-07 0.07023778 0.4445922 0.3211783 0.5695721
## chromosome5 chromosome6 chromosome7 chromosome8 chromosome9
## Petalura 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
## Uropetala 0.7261577 0.1637175 0.5288944 0.5991783 0.5828773
## mean_substitution_rate chromosome1:mean_substitution_rate
## Petalura 0.51516342 0.49893492
## Uropetala 0.02240144 0.01518673
## chromosome2:mean_substitution_rate chromosome3:mean_substitution_rate
## Petalura 0.5032458 0.51411087
## Uropetala 0.3502234 0.04367429
## chromosome4:mean_substitution_rate chromosome5:mean_substitution_rate
## Petalura 0.5226187 0.5109369
## Uropetala 0.7783628 0.3010779
## chromosome6:mean_substitution_rate chromosome7:mean_substitution_rate
## Petalura 0.50611042 0.5113377
## Uropetala 0.07855671 0.3915833
## chromosome8:mean_substitution_rate chromosome9:mean_substitution_rate
## Petalura 0.4878573 0.4965593
## Uropetala 0.6520729 0.6575404this results in these retained variables
p_df <- data.frame(p)
p_petalura_br <- data.frame(factor = names(p_df), p.value = as.numeric(p_df[1,]))
p_uropetala_br <- data.frame(factor = names(p_df), p.value = as.numeric(p_df[2,]))
p_petalura_br[p_petalura_br$p.value<.05 & is.na(p_petalura_br$p.value) == F,]## factor p.value
## 1 X.Intercept. 0
## 2 chromosome1 0
## 3 chromosome2 0
## 4 chromosome3 0
## 5 chromosome4 0
## 6 chromosome5 0
## 7 chromosome6 0
## 8 chromosome7 0
## 9 chromosome8 0
## 10 chromosome9 0p_uropetala_br[p_uropetala_br$p.value<.05 & is.na(p_petalura_br$p.value) == F,]## factor p.value
## 1 X.Intercept. 1.574657e-07
## 11 mean_substitution_rate 2.240144e-02
## 12 chromosome1.mean_substitution_rate 1.518673e-02
## 14 chromosome3.mean_substitution_rate 4.367429e-02or
lrt
library(afex)
library(car)## Loading required package: carData##
## Attaching package: 'car'## The following object is masked from 'package:dplyr':
##
## recodeAnova(multinom_model_br,type="III")## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## chromosome 33.355 18 0.01512 *
## mean_substitution_rate 8.074 2 0.01765 *
## chromosome:mean_substitution_rate 33.928 18 0.01286 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1compare to treatment coding to see what happens
set_treatment_contrasts() # ## setting contr.treatment globally: options(contrasts=c('contr.treatment', 'contr.poly'))multinom_model_br <- multinom(best_relationship ~ chromosome*mean_substitution_rate , data = likelihoods)## # weights: 63 (40 variable)
## initial value 926.130159
## iter 10 value 644.110007
## iter 20 value 628.548572
## iter 30 value 626.352009
## iter 40 value 624.878205
## iter 50 value 624.590396
## iter 60 value 624.587150
## final value 624.587138
## convergedAnova(multinom_model_br,type="III")## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## chromosome 33.355 18 0.01512 *
## mean_substitution_rate 3.789 2 0.15041
## chromosome:mean_substitution_rate 33.928 18 0.01286 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1do for each
set_sum_contrasts() ## setting contr.sum globally: options(contrasts=c('contr.sum', 'contr.poly'))for(i in 1:nlevels(likelihoods$chromosome)){
print(levels(likelihoods$chromosome)[i])
multinom_model_br_chromosome <- multinom(best_relationship ~mean_substitution_rate , data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],])
print(Anova(multinom_model_br_chromosome,type="III"))
print(summary(multinom_model_br_chromosome))
print(exp(coef(multinom_model_br_chromosome))
)
}## [1] "chr_HiC_scaffold_1"
## # weights: 9 (4 variable)
## initial value 137.326536
## iter 10 value 104.632537
## iter 10 value 104.632537
## final value 104.632537
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 3.7888 2 0.1504
## Call:
## multinom(formula = best_relationship ~ mean_substitution_rate,
## data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],
## ])
##
## Coefficients:
## (Intercept) mean_substitution_rate
## Petalura -0.5758698 -0.2848090
## Uropetala -2.1505901 0.1654807
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## Petalura 0.4278047 0.2186189
## Uropetala 0.4757895 0.1575405
##
## Residual Deviance: 209.2651
## AIC: 217.2651
## (Intercept) mean_substitution_rate
## Petalura 0.5622156 0.7521579
## Uropetala 0.1164154 1.1799602
## [1] "chr_HiC_scaffold_2"
## # weights: 9 (4 variable)
## initial value 150.509884
## iter 10 value 113.376162
## iter 10 value 113.376162
## final value 113.376162
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 1.7143 2 0.4244
## Call:
## multinom(formula = best_relationship ~ mean_substitution_rate,
## data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],
## ])
##
## Coefficients:
## (Intercept) mean_substitution_rate
## Petalura -0.7808834 -0.20857596
## Uropetala -1.6345863 -0.09768767
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## Petalura 0.3793110 0.1811273
## Uropetala 0.4683687 0.2019119
##
## Residual Deviance: 226.7523
## AIC: 234.7523
## (Intercept) mean_substitution_rate
## Petalura 0.4580013 0.8117394
## Uropetala 0.1950330 0.9069321
## [1] "chr_HiC_scaffold_3"
## # weights: 9 (4 variable)
## initial value 58.226451
## iter 10 value 43.001426
## iter 10 value 43.001426
## final value 43.001426
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 0.84738 2 0.6546
## Call:
## multinom(formula = best_relationship ~ mean_substitution_rate,
## data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],
## ])
##
## Coefficients:
## (Intercept) mean_substitution_rate
## Petalura -1.624534 -0.02114063
## Uropetala -1.934871 0.24428411
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## Petalura 0.8075783 0.3632684
## Uropetala 0.7049686 0.2665417
##
## Residual Deviance: 86.00285
## AIC: 94.00285
## (Intercept) mean_substitution_rate
## Petalura 0.1970034 0.9790813
## Uropetala 0.1444429 1.2767070
## [1] "chr_HiC_scaffold_3_HiC_scaffold_4"
## # weights: 9 (4 variable)
## initial value 73.607023
## iter 10 value 59.841548
## iter 10 value 59.841548
## final value 59.841548
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 1.5086 2 0.4703
## Call:
## multinom(formula = best_relationship ~ mean_substitution_rate,
## data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],
## ])
##
## Coefficients:
## (Intercept) mean_substitution_rate
## Petalura -1.2062699 0.1272349
## Uropetala -0.8379892 -0.4311798
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## Petalura 0.5794926 0.2591841
## Uropetala 0.7951948 0.4644393
##
## Residual Deviance: 119.6831
## AIC: 127.6831
## (Intercept) mean_substitution_rate
## Petalura 0.2993116 1.1356838
## Uropetala 0.4325795 0.6497421
## [1] "chr_HiC_scaffold_4"
## # weights: 9 (4 variable)
## initial value 148.312659
## iter 10 value 85.962824
## final value 83.956857
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 4.2909 2 0.117
## Call:
## multinom(formula = best_relationship ~ mean_substitution_rate,
## data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],
## ])
##
## Coefficients:
## (Intercept) mean_substitution_rate
## Petalura -1.831258 -0.07444693
## Uropetala -1.038815 -0.74656194
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## Petalura 0.4829316 0.2124352
## Uropetala 0.6704813 0.4492962
##
## Residual Deviance: 167.9137
## AIC: 175.9137
## (Intercept) mean_substitution_rate
## Petalura 0.1602119 0.9282567
## Uropetala 0.3538738 0.4739934
## [1] "chr_HiC_scaffold_5"
## # weights: 9 (4 variable)
## initial value 150.509884
## iter 10 value 95.641197
## final value 95.641162
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 7.4797 2 0.02376 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Call:
## multinom(formula = best_relationship ~ mean_substitution_rate,
## data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],
## ])
##
## Coefficients:
## (Intercept) mean_substitution_rate
## Petalura -1.2986154 -0.1587395
## Uropetala -0.1768951 -1.2973934
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## Petalura 0.4441454 0.2170341
## Uropetala 0.8311062 0.6103830
##
## Residual Deviance: 191.2823
## AIC: 199.2823
## (Intercept) mean_substitution_rate
## Petalura 0.2729094 0.8532186
## Uropetala 0.8378677 0.2732431
## [1] "chr_HiC_scaffold_6"
## # weights: 9 (4 variable)
## initial value 78.001472
## iter 10 value 52.601963
## final value 52.601958
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 0.1456 2 0.9298
## Call:
## multinom(formula = best_relationship ~ mean_substitution_rate,
## data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],
## ])
##
## Coefficients:
## (Intercept) mean_substitution_rate
## Petalura -1.646763 -0.06797798
## Uropetala -1.631746 -0.07644125
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## Petalura 0.5900727 0.2585611
## Uropetala 0.5921235 0.2620506
##
## Residual Deviance: 105.2039
## AIC: 113.2039
## (Intercept) mean_substitution_rate
## Petalura 0.1926726 0.9342810
## Uropetala 0.1955879 0.9264073
## [1] "chr_HiC_scaffold_7"
## # weights: 9 (4 variable)
## initial value 75.804248
## iter 10 value 46.371354
## final value 46.370749
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 3.9215 2 0.1408
## Call:
## multinom(formula = best_relationship ~ mean_substitution_rate,
## data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],
## ])
##
## Coefficients:
## (Intercept) mean_substitution_rate
## Petalura -1.1504053 -0.4847574
## Uropetala -0.9122891 -0.4758929
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## Petalura 0.7827928 0.4385372
## Uropetala 0.7003460 0.3873423
##
## Residual Deviance: 92.7415
## AIC: 100.7415
## (Intercept) mean_substitution_rate
## Petalura 0.3165085 0.6158466
## Uropetala 0.4016039 0.6213300
## [1] "chr_HiC_scaffold_9"
## # weights: 9 (4 variable)
## initial value 28.563920
## iter 10 value 10.080283
## iter 20 value 9.618965
## iter 30 value 9.456753
## iter 40 value 9.382564
## iter 50 value 9.233983
## iter 60 value 9.223919
## iter 70 value 9.209476
## iter 80 value 9.195118
## iter 90 value 9.173450
## iter 100 value 9.148728
## final value 9.148728
## stopped after 100 iterations
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 13.889 2 0.0009637 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Call:
## multinom(formula = best_relationship ~ mean_substitution_rate,
## data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],
## ])
##
## Coefficients:
## (Intercept) mean_substitution_rate
## Petalura -66.332004 16.21691757
## Uropetala -1.838928 -0.06931592
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## Petalura 73.515642 18.0122492
## Uropetala 1.260246 0.6972358
##
## Residual Deviance: 18.29746
## AIC: 26.29746
## (Intercept) mean_substitution_rate
## Petalura 1.557316e-29 1.103870e+07
## Uropetala 1.589878e-01 9.330319e-01
## [1] "not_localized_to_chromosome"
## # weights: 9 (4 variable)
## initial value 25.268083
## iter 10 value 16.131530
## final value 16.123097
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 1.7626 2 0.4142
## Call:
## multinom(formula = best_relationship ~ mean_substitution_rate,
## data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],
## ])
##
## Coefficients:
## (Intercept) mean_substitution_rate
## Petalura -0.8338776 -1.7416775
## Uropetala -0.4332941 -0.3385221
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## Petalura 2.0133564 2.1951540
## Uropetala 0.8154098 0.4485521
##
## Residual Deviance: 32.24619
## AIC: 40.24619
## (Intercept) mean_substitution_rate
## Petalura 0.4343617 0.1752262
## Uropetala 0.6483698 0.7128230compare here to show the same
set_treatment_contrasts() ## setting contr.treatment globally: options(contrasts=c('contr.treatment', 'contr.poly'))for(i in 1:nlevels(likelihoods$chromosome)){
print(levels(likelihoods$chromosome)[i])
multinom_model_br_chromosome <- multinom(best_relationship ~mean_substitution_rate , data = likelihoods[likelihoods$chromosome == levels(likelihoods$chromosome)[i],])
print(Anova(multinom_model_br_chromosome,type="III"))
}## [1] "chr_HiC_scaffold_1"
## # weights: 9 (4 variable)
## initial value 137.326536
## iter 10 value 104.632537
## iter 10 value 104.632537
## final value 104.632537
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 3.7888 2 0.1504
## [1] "chr_HiC_scaffold_2"
## # weights: 9 (4 variable)
## initial value 150.509884
## iter 10 value 113.376162
## iter 10 value 113.376162
## final value 113.376162
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 1.7143 2 0.4244
## [1] "chr_HiC_scaffold_3"
## # weights: 9 (4 variable)
## initial value 58.226451
## iter 10 value 43.001426
## iter 10 value 43.001426
## final value 43.001426
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 0.84738 2 0.6546
## [1] "chr_HiC_scaffold_3_HiC_scaffold_4"
## # weights: 9 (4 variable)
## initial value 73.607023
## iter 10 value 59.841548
## iter 10 value 59.841548
## final value 59.841548
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 1.5086 2 0.4703
## [1] "chr_HiC_scaffold_4"
## # weights: 9 (4 variable)
## initial value 148.312659
## iter 10 value 85.962824
## final value 83.956857
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 4.2909 2 0.117
## [1] "chr_HiC_scaffold_5"
## # weights: 9 (4 variable)
## initial value 150.509884
## iter 10 value 95.641197
## final value 95.641162
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 7.4797 2 0.02376 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] "chr_HiC_scaffold_6"
## # weights: 9 (4 variable)
## initial value 78.001472
## iter 10 value 52.601963
## final value 52.601958
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 0.1456 2 0.9298
## [1] "chr_HiC_scaffold_7"
## # weights: 9 (4 variable)
## initial value 75.804248
## iter 10 value 46.371354
## final value 46.370749
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 3.9215 2 0.1408
## [1] "chr_HiC_scaffold_9"
## # weights: 9 (4 variable)
## initial value 28.563920
## iter 10 value 10.080283
## iter 20 value 9.618965
## iter 30 value 9.456753
## iter 40 value 9.382564
## iter 50 value 9.233983
## iter 60 value 9.223919
## iter 70 value 9.209476
## iter 80 value 9.195118
## iter 90 value 9.173450
## iter 100 value 9.148728
## final value 9.148728
## stopped after 100 iterations
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 13.889 2 0.0009637 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] "not_localized_to_chromosome"
## # weights: 9 (4 variable)
## initial value 25.268083
## iter 10 value 16.131530
## final value 16.123097
## converged
## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 1.7626 2 0.4142interpretation
look at exponents - <0 means moving to reference level (phenes)
coef(multinom_model_br)## (Intercept) chromosomechr_HiC_scaffold_2 chromosomechr_HiC_scaffold_3
## Petalura -0.576048 -0.2047666 -1.0480125
## Uropetala -2.150751 0.5161748 0.2159985
## chromosomechr_HiC_scaffold_3_HiC_scaffold_4
## Petalura -0.6302126
## Uropetala 1.3128388
## chromosomechr_HiC_scaffold_4 chromosomechr_HiC_scaffold_5
## Petalura -1.255165 -0.7227215
## Uropetala 1.112074 1.9739324
## chromosomechr_HiC_scaffold_6 chromosomechr_HiC_scaffold_7
## Petalura -1.0706886 -0.574364
## Uropetala 0.5192417 1.238481
## chromosomechr_HiC_scaffold_9 chromosomenot_localized_to_chromosome
## Petalura -307.4642007 -0.2579043
## Uropetala 0.2496454 1.7175522
## mean_substitution_rate
## Petalura -0.2847222
## Uropetala 0.1655234
## chromosomechr_HiC_scaffold_2:mean_substitution_rate
## Petalura 0.07614703
## Uropetala -0.26318332
## chromosomechr_HiC_scaffold_3:mean_substitution_rate
## Petalura 0.2633879
## Uropetala 0.0788177
## chromosomechr_HiC_scaffold_3_HiC_scaffold_4:mean_substitution_rate
## Petalura 0.4119496
## Uropetala -0.5967561
## chromosomechr_HiC_scaffold_4:mean_substitution_rate
## Petalura 0.2102528
## Uropetala -0.9122328
## chromosomechr_HiC_scaffold_5:mean_substitution_rate
## Petalura 0.1260941
## Uropetala -1.4629376
## chromosomechr_HiC_scaffold_6:mean_substitution_rate
## Petalura 0.2167400
## Uropetala -0.2420499
## chromosomechr_HiC_scaffold_7:mean_substitution_rate
## Petalura -0.2000363
## Uropetala -0.6414500
## chromosomechr_HiC_scaffold_9:mean_substitution_rate
## Petalura 75.0298561
## Uropetala -0.1934146
## chromosomenot_localized_to_chromosome:mean_substitution_rate
## Petalura -1.4568599
## Uropetala -0.5040987or consider odds ratio/rr (check this)
exp(coef(multinom_model_br))## (Intercept) chromosomechr_HiC_scaffold_2 chromosomechr_HiC_scaffold_3
## Petalura 0.5621155 0.8148375 0.3506339
## Uropetala 0.1163967 1.6756059 1.2411005
## chromosomechr_HiC_scaffold_3_HiC_scaffold_4
## Petalura 0.5324786
## Uropetala 3.7167098
## chromosomechr_HiC_scaffold_4 chromosomechr_HiC_scaffold_5
## Petalura 0.2850289 0.4854293
## Uropetala 3.0406571 7.1989303
## chromosomechr_HiC_scaffold_6 chromosomechr_HiC_scaffold_7
## Petalura 0.3427724 0.5630629
## Uropetala 1.6807526 3.4503675
## chromosomechr_HiC_scaffold_9 chromosomenot_localized_to_chromosome
## Petalura 2.95117e-134 0.7726692
## Uropetala 1.28357e+00 5.5708756
## mean_substitution_rate
## Petalura 0.7522232
## Uropetala 1.1800105
## chromosomechr_HiC_scaffold_2:mean_substitution_rate
## Petalura 1.079121
## Uropetala 0.768601
## chromosomechr_HiC_scaffold_3:mean_substitution_rate
## Petalura 1.301331
## Uropetala 1.082007
## chromosomechr_HiC_scaffold_3_HiC_scaffold_4:mean_substitution_rate
## Petalura 1.5097583
## Uropetala 0.5505948
## chromosomechr_HiC_scaffold_4:mean_substitution_rate
## Petalura 1.2339900
## Uropetala 0.4016265
## chromosomechr_HiC_scaffold_5:mean_substitution_rate
## Petalura 1.134389
## Uropetala 0.231555
## chromosomechr_HiC_scaffold_6:mean_substitution_rate
## Petalura 1.242021
## Uropetala 0.785017
## chromosomechr_HiC_scaffold_7:mean_substitution_rate
## Petalura 0.8187010
## Uropetala 0.5265284
## chromosomechr_HiC_scaffold_9:mean_substitution_rate
## Petalura 3.846383e+32
## Uropetala 8.241402e-01
## chromosomenot_localized_to_chromosome:mean_substitution_rate
## Petalura 0.2329667
## Uropetala 0.6040498graphs
set_treatment_contrasts() # use sum coding, necessary to make type III LR tests valid## setting contr.treatment globally: options(contrasts=c('contr.treatment', 'contr.poly'))multinom_model_br <- multinom(best_relationship ~ chromosome*mean_substitution_rate , data = likelihoods)## # weights: 63 (40 variable)
## initial value 926.130159
## iter 10 value 644.110007
## iter 20 value 628.548572
## iter 30 value 626.352009
## iter 40 value 624.878205
## iter 50 value 624.590396
## iter 60 value 624.587150
## final value 624.587138
## convergedlibrary(ggeffects)
pprob_pct_ctry <- ggeffect(multinom_model_br, terms = "mean_substitution_rate[0:10 by = 1]")
# Build the plot with ggplot manually
# The aesthetics refer to variable names in the ggeffects saved results
# We are grouping the plot by the "response.level" of our outcome.
ggplot(data = pprob_pct_ctry, aes(x = x, y = predicted,
color = response.level, group = response.level)) +
# Add line layer
geom_line() +
# Add point layer
geom_point() +
# Add confidence intervals as error bars
geom_errorbar(aes(ymin = conf.low, ymax = conf.high,
color = response.level,
group = response.level),
width = .1) +
# Change the color of the lines, remove legend title, change the
# labels of the lines in the legend.
scale_color_brewer(palette = "Dark2",
name = "",
labels = c("Petalura",
"Phenes",
"Uropetala")) +
# Add titles to the x and y axis
labs(
x = "Mean Nucleotide Substitution Rate",
y = "Probability"
) +
# Set the theme
theme_minimal() +
theme(text = element_text(family = "Times New Roman")) +
theme(
legend.position = "bottom", # move legend to the bottom
axis.title = element_text(size = 14) # increase axis title size
)
pprob_pct_ctry <- ggeffect(multinom_model_br, terms = "chromosome")
# Build the plot with ggplot manually
# The aesthetics refer to variable names in the ggeffects saved results
# We are grouping the plot by the "response.level" of our outcome.
ggplot(data = pprob_pct_ctry, aes(x = x, y = predicted,
color = response.level, group = response.level)) +
# Add line layer
geom_line() +
# Add point layer
geom_point() +
# Add confidence intervals as error bars
geom_errorbar(aes(ymin = conf.low, ymax = conf.high,
color = response.level,
group = response.level),
width = .1) +
# Change the color of the lines, remove legend title, change the
# labels of the lines in the legend.
scale_color_brewer(palette = "Dark2",
name = "",
labels = c("Petalura",
"Phenes", "Uropetala")) +
# Add titles to the x and y axis
labs(
x = "Chromosome",
y = "Probability"
) +
# Set the theme
theme_minimal() +
theme(
legend.position = "bottom", # move legend to the bottom
axis.title = element_text(size = 14) # increase axis title size
) +
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1)) +
theme(text = element_text(family = "Times New Roman")) +
scale_x_discrete(labels=c('Chromosome One', 'Chromosome two',
'Chromosome three', 'Chromosome three/four',
'Chromosome four', 'Chromosome five', 'Chromosome six',
'chromosome seven', 'Micro chromosome', 'Sex chromosome',
'Not localized to chromosome', 'Not recovered in genome'))
plot(likelihoods$mean_substitution_rate)
head(pp <- fitted(multinom_model_br))## Phenes Petalura Uropetala
## 1 0.7658821 0.1604014 0.07371648
## 2 0.7416264 0.1290317 0.12934190
## 3 0.7349767 0.1629629 0.10206043
## 4 0.6665760 0.2215455 0.11187846
## 5 0.7224305 0.1215501 0.15601942
## 6 0.6620377 0.2255505 0.11241179dses <- data.frame(chromosome = levels(likelihoods$chromosome), mean_substitution_rate = mean(likelihoods$mean_substitution_rate))
predict(multinom_model_br, newdata = dses, "probs")## Phenes Petalura Uropetala
## 1 0.6738630 2.179904e-01 0.10814663
## 2 0.6816935 2.083059e-01 0.11000066
## 3 0.7036292 1.330586e-01 0.16331220
## 4 0.6367440 2.439596e-01 0.11929643
## 5 0.8184922 1.134925e-01 0.06801531
## 6 0.7885564 1.581593e-01 0.05328430
## 7 0.7476638 1.262535e-01 0.12608268
## 8 0.7794073 9.629404e-02 0.12429864
## 9 0.8760159 1.433699e-71 0.12398410
## 10 0.7402305 1.094979e-02 0.24881968span <- 0:10
dwrite <- data.frame(chromosome = rep(c(levels(likelihoods$chromosome)), each = length(span)), mean_substitution_rate = rep(span,
nlevels(likelihoods$chromosome)))
## store the predicted probabilities for each value of ses and write
pp.write <- cbind(dwrite, predict(multinom_model_br, newdata = dwrite, type = "probs", se = TRUE))
## calculate the mean probabilities within each level of ses
by(pp.write[, 3:5], pp.write$chromosome, colMeans)## pp.write$chromosome: chr_HiC_scaffold_1
## Phenes Petalura Uropetala
## 0.6683947 0.1294275 0.2021778
## ------------------------------------------------------------
## pp.write$chromosome: chr_HiC_scaffold_2
## Phenes Petalura Uropetala
## 0.76603994 0.14125903 0.09270103
## ------------------------------------------------------------
## pp.write$chromosome: chr_HiC_scaffold_3
## Phenes Petalura Uropetala
## 0.5787744 0.1042683 0.3169573
## ------------------------------------------------------------
## pp.write$chromosome: chr_HiC_scaffold_3_HiC_scaffold_4
## Phenes Petalura Uropetala
## 0.58493796 0.34760060 0.06746144
## ------------------------------------------------------------
## pp.write$chromosome: chr_HiC_scaffold_4
## Phenes Petalura Uropetala
## 0.85990710 0.09565700 0.04443591
## ------------------------------------------------------------
## pp.write$chromosome: chr_HiC_scaffold_5
## Phenes Petalura Uropetala
## 0.83535014 0.10799179 0.05665806
## ------------------------------------------------------------
## pp.write$chromosome: chr_HiC_scaffold_6
## Phenes Petalura Uropetala
## 0.7845330 0.1089557 0.1065112
## ------------------------------------------------------------
## pp.write$chromosome: chr_HiC_scaffold_7
## Phenes Petalura Uropetala
## 0.87843512 0.05307897 0.06848591
## ------------------------------------------------------------
## pp.write$chromosome: chr_HiC_scaffold_9
## Phenes Petalura Uropetala
## 0.39823373 0.54546387 0.05630241
## ------------------------------------------------------------
## pp.write$chromosome: not_localized_to_chromosome
## Phenes Petalura Uropetala
## 0.8367809 0.0245696 0.1386495library(reshape2)##
## Attaching package: 'reshape2'## The following object is masked from 'package:tidyr':
##
## smithslpp <- melt(pp.write, id.vars = c("chromosome", "mean_substitution_rate"), value.name = "probability")
head(lpp)## chromosome mean_substitution_rate variable probability
## 1 chr_HiC_scaffold_1 0 Phenes 0.5957657
## 2 chr_HiC_scaffold_1 1 Phenes 0.6409494
## 3 chr_HiC_scaffold_1 2 Phenes 0.6756113
## 4 chr_HiC_scaffold_1 3 Phenes 0.6990532
## 5 chr_HiC_scaffold_1 4 Phenes 0.7114144
## 6 chr_HiC_scaffold_1 5 Phenes 0.7134292ggplot(lpp, aes(x = mean_substitution_rate, y = probability, colour = chromosome)) + geom_line() + facet_grid(variable ~
., scales = "free")
pprob_pct_ctry_new <- ggeffect(multinom_model_br, dwrite)
ggplot(pprob_pct_ctry_new, aes(x = group, y = predicted, colour = x)) + geom_line() +
facet_wrap(~response.level, scales = "free", ncol=1)+
geom_errorbar(aes(ymin = conf.low, ymax = conf.high,
width = .1), color="black")
petalura
eda
what does this look like?
ggplot(likelihoods, aes(x = mean_substitution_rate, fill=best_relationship_Petalura)) +
geom_histogram()## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
# theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))pie charts
data <- data.frame(
group=c("Sister to gigantea and litorea", "Sister to Ingentissima", "Sister to the Rest of Uropetala"),
value=c(43,797,83)
)
ggplot(data, aes(x="", y=value, fill=group)) +
geom_bar(stat="identity", width=1) +
coord_polar("y", start=0) +
theme_void() 
pie_data <- data.frame(table(likelihoods_pie$best_relationship_Petalura))
pie_data## Var1 Freq
## 1 gigantea_litorea 43
## 2 ingentissima 781
## 3 Sister 83
## 4 Unclear 16clean up
pie_data$Group <- revalue(pie_data$Var1,
c("gigantea_litorea" ="Sister to *P. gigantea* and *P. litorea*",
"ingentissima" = "Sister to *P. ingentissima*",
"Sister" = "Sister to the rest of *Uropetala*"))
ggplot(pie_data, aes(x="", y=Freq, fill=Group)) +
geom_bar(stat="identity", width=1) +
coord_polar("y", start=0) +
theme_void() +
labs(fill= "Clade placement")+
theme(
legend.text = element_markdown(color = "black", size = 11)
)
analysis
lots of help @ https://stats.oarc.ucla.edu/r/dae/multinomial-logistic-regression/
set reference level and remove unclear
likelihoods$best_relationship_Petalura <- as.factor(likelihoods$best_relationship_Petalura)
likelihoods$best_relationship_Petalura <- relevel(likelihoods$best_relationship_Petalura, ref = "ingentissima")
likelihoods <- likelihoods %>%
dplyr::filter(best_relationship_Petalura != "Unclear")
likelihoods$best_relationship_Petalura <- factor(likelihoods$best_relationship_Petalura)develop model
run model
set_sum_contrasts()## setting contr.sum globally: options(contrasts=c('contr.sum', 'contr.poly'))multinom_model_br_pet <- multinom(best_relationship_Petalura ~ mean_substitution_rate , data = likelihoods)## # weights: 9 (4 variable)
## initial value 925.031547
## iter 10 value 421.021163
## iter 20 value 390.245280
## final value 390.245133
## convergedsummary(multinom_model_br_pet)## Call:
## multinom(formula = best_relationship_Petalura ~ mean_substitution_rate,
## data = likelihoods)
##
## Coefficients:
## (Intercept) mean_substitution_rate
## gigantea_litorea -2.427076 -0.31357687
## Sister -2.461459 0.05517237
##
## Std. Errors:
## (Intercept) mean_substitution_rate
## gigantea_litorea 0.3262380 0.18214200
## Sister 0.1916925 0.06972866
##
## Residual Deviance: 780.4903
## AIC: 788.4903assumptions
linear relationship between predictor and modeled outcome (logit)
# Select only outcome and numeric predictors
# drop missing and save in new dataset
df_model <- likelihoods %>%
dplyr::select("mean_substitution_rate") %>% # enter numeric variables
drop_na(mean_substitution_rate) # drop cases with missing values on these variables.
# save names of predictors to plug into command below.
predictors <- colnames(df_model)
# Save predicted probabilities
df_model$probabilities <- multinom_model_br_pet$fitted.values[,1]
# Manually calculate the logit values and tidy data for the plot
df_model <- df_model %>%
mutate(logit = log(probabilities/(1-probabilities))) %>%
dplyr::select(-probabilities) %>%
gather(key = "predictors", value = "predictor.value", -logit)
ggplot(df_model, aes(y = logit, x = predictor.value))+
geom_point(size = 0.5, alpha = 0.5) +
geom_smooth(method = "loess") +
theme_bw() +
facet_wrap(~predictors, scales = "free_x")## `geom_smooth()` using formula = 'y ~ x'
results
wald tests
z <- summary(multinom_model_br_pet)$coefficients/summary(multinom_model_br_pet)$standard.errors
z## (Intercept) mean_substitution_rate
## gigantea_litorea -7.439589 -1.7216066
## Sister -12.840663 0.7912438p <- (1 - pnorm(abs(z), 0, 1)) * 2
p## (Intercept) mean_substitution_rate
## gigantea_litorea 1.010303e-13 0.0851408
## Sister 0.000000e+00 0.4288018this results in these retained variables
p_df <- data.frame(p)
p_petalura_br_pet <- data.frame(factor = names(p_df), p.value = as.numeric(p_df[1,]))
p_uropetala_br_pet <- data.frame(factor = names(p_df), p.value = as.numeric(p_df[2,]))
p_petalura_br_pet[p_petalura_br_pet$p.value<.05 & is.na(p_petalura_br_pet$p.value) == F,]## factor p.value
## 1 X.Intercept. 1.010303e-13p_uropetala_br_pet[p_uropetala_br_pet$p.value<.05 & is.na(p_petalura_br_pet$p.value) == F,]## factor p.value
## 1 X.Intercept. 0lrt
Anova(multinom_model_br_pet,type="III")## Analysis of Deviance Table (Type III tests)
##
## Response: best_relationship_Petalura
## LR Chisq Df Pr(>Chisq)
## mean_substitution_rate 4.7061 2 0.09508 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1interpretation
look at exponents - <0 means moving to reference level (phenes)
coef(multinom_model_br_pet)## (Intercept) mean_substitution_rate
## gigantea_litorea -2.427076 -0.31357687
## Sister -2.461459 0.05517237consider odds ratio/rr (check this)
exp(coef(multinom_model_br_pet))## (Intercept) mean_substitution_rate
## gigantea_litorea 0.08829461 0.7308282
## Sister 0.08531040 1.0567227graph
library(ggeffects)
pprob_pct_ctry <- ggeffect(multinom_model_br_pet, terms = "mean_substitution_rate[0:10 by = 1]")
# Build the plot with ggplot manually
# The aesthetics refer to variable names in the ggeffects saved results
# We are grouping the plot by the "response.level" of our outcome.
ggplot(data = pprob_pct_ctry, aes(x = x, y = predicted,
color = response.level, group = response.level)) +
# Add line layer
geom_line() +
# Add point layer
geom_point() +
# Add confidence intervals as error bars
geom_errorbar(aes(ymin = conf.low, ymax = conf.high,
color = response.level,
group = response.level),
width = .1) +
# Change the color of the lines, remove legend title, change the
# labels of the lines in the legend.
scale_color_brewer(palette = "Dark2",
name = "",
labels = c("Sister to Petalura gigantea and Petalura litorea",
"Sister to Petalura ingentissima",
"Sister to all other Petalura")) +
# Add titles to the x and y axis
labs(
x = "Mean Nucleotide Substitution Rate",
y = "Probability"
) +
# Set the theme
theme_minimal() +
theme(text = element_text(family = "Times New Roman")) +
theme(
legend.position = "bottom", # move legend to the bottom
axis.title = element_text(size = 14) # increase axis title size
)
head(pp <- fitted(multinom_model_br_pet))## ingentissima gigantea_litorea Sister
## 1 0.8727008 0.04567246 0.08162675
## 2 0.8712158 0.04804272 0.08074147
## 3 0.8825946 0.02618151 0.09122391
## 4 0.8715504 0.04751437 0.08093525
## 5 0.8693068 0.05100239 0.07969082
## 6 0.8704423 0.04925279 0.08030493dses <- data.frame(chromosome = levels(likelihoods$chromosome), mean_substitution_rate = mean(likelihoods$mean_substitution_rate))
predict(multinom_model_br_pet, newdata = dses, "probs")## ingentissima gigantea_litorea Sister
## 1 0.874898 0.04202631 0.08307572
## 2 0.874898 0.04202631 0.08307572
## 3 0.874898 0.04202631 0.08307572
## 4 0.874898 0.04202631 0.08307572
## 5 0.874898 0.04202631 0.08307572
## 6 0.874898 0.04202631 0.08307572
## 7 0.874898 0.04202631 0.08307572
## 8 0.874898 0.04202631 0.08307572
## 9 0.874898 0.04202631 0.08307572
## 10 0.874898 0.04202631 0.08307572span <- 0:10
dwrite <- data.frame(mean_substitution_rate = rep(span))
## store the predicted probabilities for each value of ses and write
pp.write <- cbind(dwrite, predict(multinom_model_br_pet, newdata = dwrite, type = "probs", se = TRUE))
## calculate the mean probabilities within each level of ses
#by(pp.write[, 2:4], colMeans)library(reshape2)
lpp <- melt(pp.write, id.vars = c("mean_substitution_rate"), value.name = "probability")
head(lpp)## mean_substitution_rate variable probability
## 1 0 ingentissima 0.8520754
## 2 1 ingentissima 0.8660426
## 3 2 ingentissima 0.8753333
## 4 3 ingentissima 0.8809551
## 5 4 ingentissima 0.8837320
## 6 5 ingentissima 0.8843150ggplot(lpp, aes(x = mean_substitution_rate, y = probability)) +
geom_line() +
facet_grid(variable ~ ., scales = "free")
ggplot(lpp, aes(x = mean_substitution_rate, color=variable, y = probability)) +
geom_line() 
original approach
added to compare for genus
#filter for only significant interactions
#install.packages("kableExtra")
library(kableExtra)##
## Attaching package: 'kableExtra'## The following object is masked from 'package:dplyr':
##
## group_rowslibrary(broom)
#install.packages("gtsummary")
library(gtsummary)##
## Attaching package: 'gtsummary'## The following object is masked from 'package:plyr':
##
## mutateset_treatment_contrasts()## setting contr.treatment globally: options(contrasts=c('contr.treatment', 'contr.poly'))multinom_model <- multinom(best_relationship ~ chromosome*mean_substitution_rate + mean_substitution_rate + chromosome, data = likelihoods)## # weights: 63 (40 variable)
## initial value 925.031547
## iter 10 value 643.939374
## iter 20 value 628.146881
## iter 30 value 625.943762
## iter 40 value 624.470980
## iter 50 value 624.173493
## iter 60 value 624.169706
## final value 624.169692
## convergedtidy(multinom_model, conf.int = TRUE) ## # A tibble: 40 × 8
## y.level term estimate std.error statistic p.value conf.low conf.high
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Petalura (Intercept) -0.576 0.428 -1.35 1.78e- 1 -1.41 2.62e-1
## 2 Petalura chromosome… -0.188 0.572 -0.328 7.43e- 1 -1.31 9.34e-1
## 3 Petalura chromosome… -1.05 0.914 -1.15 2.52e- 1 -2.84 7.43e-1
## 4 Petalura chromosome… -0.630 0.720 -0.875 3.82e- 1 -2.04 7.82e-1
## 5 Petalura chromosome… -1.26 0.645 -1.95 5.17e- 2 -2.52 9.36e-3
## 6 Petalura chromosome… -0.723 0.617 -1.17 2.41e- 1 -1.93 4.86e-1
## 7 Petalura chromosome… -1.07 0.729 -1.47 1.42e- 1 -2.50 3.58e-1
## 8 Petalura chromosome… -0.574 0.892 -0.644 5.20e- 1 -2.32 1.17e+0
## 9 Petalura chromosome… -312. 23.9 -13.1 5.98e-39 -359. -2.65e+2
## 10 Petalura chromosome… -0.258 2.06 -0.125 9.00e- 1 -4.29 3.78e+0
## # ℹ 30 more rowsmodel_summary <- tidy(multinom_model, conf.int = TRUE, exponentiate = TRUE)
model_summary## # A tibble: 40 × 8
## y.level term estimate std.error statistic p.value conf.low conf.high
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Petalura (Interce… 5.62e- 1 0.428 -1.35 1.78e- 1 2.43e- 1 1.30e+ 0
## 2 Petalura chromoso… 8.29e- 1 0.572 -0.328 7.43e- 1 2.70e- 1 2.54e+ 0
## 3 Petalura chromoso… 3.51e- 1 0.914 -1.15 2.52e- 1 5.85e- 2 2.10e+ 0
## 4 Petalura chromoso… 5.33e- 1 0.720 -0.875 3.82e- 1 1.30e- 1 2.18e+ 0
## 5 Petalura chromoso… 2.85e- 1 0.645 -1.95 5.17e- 2 8.05e- 2 1.01e+ 0
## 6 Petalura chromoso… 4.85e- 1 0.617 -1.17 2.41e- 1 1.45e- 1 1.63e+ 0
## 7 Petalura chromoso… 3.43e- 1 0.729 -1.47 1.42e- 1 8.22e- 2 1.43e+ 0
## 8 Petalura chromoso… 5.63e- 1 0.892 -0.644 5.20e- 1 9.80e- 2 3.24e+ 0
## 9 Petalura chromoso… 4.04e-136 23.9 -13.1 5.98e-39 1.90e-156 8.58e-116
## 10 Petalura chromoso… 7.73e- 1 2.06 -0.125 9.00e- 1 1.37e- 2 4.37e+ 1
## # ℹ 30 more rowsmodel_sum <- model_summary %>%
filter(p.value < .05)
model_sum## # A tibble: 4 × 8
## y.level term estimate std.error statistic p.value conf.low conf.high
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Petalura chromoso… 4.04e-136 23.9 -13.1 5.98e-39 1.90e-156 8.58e-116
## 2 Uropetala (Interce… 1.16e- 1 0.476 -4.52 6.19e- 6 4.58e- 2 2.96e- 1
## 3 Uropetala chromoso… 7.20e+ 0 0.958 2.06 3.93e- 2 1.10e+ 0 4.70e+ 1
## 4 Uropetala chromoso… 2.32e- 1 0.630 -2.32 2.03e- 2 6.73e- 2 7.97e- 1######BIOGEOOGRAPHY####################
#load packages
library(optimx) # You need to have some version of optimx available
# as it is a BioGeoBEARS dependency; however, if you
# don't want to use optimx, and use optim() (from R core)
# you can set:
# BioGeoBEARS_run_object$use_optimx = FALSE
# ...everything should work either way -- NJM 2014-01-08
library(FD) # for FD::maxent() (make sure this is up-to-date)
library(snow) # (if you want to use multicore functionality; some systems/R versions prefer library(parallel), try either)
library(parallel)
#install.packages("rexpokit")
#install.packages("cladoRcpp")
library(devtools)
#devtools::install_github(repo="nmatzke/BioGeoBEARS")
library(BioGeoBEARS)
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_add_fossils_randomly_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_basics_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_calc_transition_matrices_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_classes_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_detection_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_DNA_cladogenesis_sim_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_extract_Qmat_COOmat_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_generics_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_models_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_on_multiple_trees_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_plots_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_readwrite_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_simulate_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_SSEsim_makePlots_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_SSEsim_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_stochastic_mapping_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_stratified_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/BioGeoBEARS_univ_model_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/calc_uppass_probs_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/calc_loglike_sp_v01.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/get_stratified_subbranch_top_downpass_likelihoods_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/runBSM_v1.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/stochastic_map_given_inputs.R")
source("http://phylo.wdfiles.com/local--files/biogeobears/summarize_BSM_tables_v1.R")
calc_loglike_sp = compiler::cmpfun(calc_loglike_sp_prebyte) # crucial to fix bug in uppass calculations
calc_independent_likelihoods_on_each_branch = compiler::cmpfun(calc_independent_likelihoods_on_each_branch_prebyte)#trfn="fixed.newick"
#trfn="petaluridae_only.newick"
#trfn="c"
trfn="~/Desktop/Jessica_calibrated_two/Jessica_calibrated_one/biogeobears.tre"
moref(trfn)## (((((Petalura_gigantea:13.49986884,Petalura_litoreaplate8:13.49986884):6.021369112,(Petalura_hesperia:15.45032698,Petalura_ingentissimaplate8:15.45032698):4.070910976):90.06650877,(Uropetala_carovei_filler:6.350546571,Uropetala_chiltoni1plate8:6.350546571):103.2372002):10.8475022,Phenes_raptorplate8:120.4352489):40.63146085,(Tachopteryx_thoreyi20k:61.30096985,(Tanypteryx_pryeriplate8:26.61193492,tanypteryx_R:26.61193492):34.68903493):99.76573993);tr <- read.tree(trfn)
#Now trim it down to one individual/species
#tr <- keep.tip(tr, c("Petalura_gigantea", "Petalura_litoreaplate8", "Petalura_hesperia", "Petalura_ingentissimaplate8", "Uropetala_carovei_filler", "Uropetala_chiltoni1plate8", "Phenes_raptorplate8","Tachopteryx_thoreyi20k", "tanypteryx_R", "Tanypteryx_pryeriplate8"))
#write.tree(tr, file = "~/Desktop/Jessica_calibrated_one/biogeobears.tre")
#look at the phylogenies
plot(tr)
title("Petaluridae tree")
axisPhylo() #
###SET UP MODEL####
geogfn = "~/Dropbox (AMNH)/Research/Petaluridae_phylogeny/Divergence_dating/condensed_biogeography.txt"
moref(geogfn)## 10 7 (SA EA WA NZ ENA WNA JA)
## Petalura_litoreaplate8 0100000
## Petalura_gigantea 0100000
## Petalura_hesperia 0010000
## Petalura_ingentissimaplate8 0100000
## Uropetala_carovei_filler 0001000
## Uropetala_chiltoni1plate8 0001000
## Phenes_raptorplate8 1000000
## tanypteryx_R 0000010
## Tanypteryx_pryeriplate8 0000001
## Tachopteryx_thoreyi20k 0000100tipranges = getranges_from_LagrangePHYLIP(lgdata_fn=geogfn)
#tipranges
max(rowSums(dfnums_to_numeric(tipranges@df)))## [1] 1#max_range_size = 11
# Intitialize a default model (DEC model)
BioGeoBEARS_run_object = define_BioGeoBEARS_run()
# Give BioGeoBEARS the location of the phylogeny Newick file
BioGeoBEARS_run_object$trfn = trfn
# Give BioGeoBEARS the location of the geography text file
BioGeoBEARS_run_object$geogfn = geogfn
# Input the maximum range size
BioGeoBEARS_run_object$max_range_size = 3
# Min to treat tip as a direct ancestor (no speciation event)
#BioGeoBEARS_run_object$min_branchlength = 0.000001 # Min to treat tip as a direct ancestor (no speciation event)
# set to FALSE for e.g. DEC* model, DEC*+J, etc.
BioGeoBEARS_run_object$include_null_range = FALSE # set to FALSE for e.g. DEC* model, DEC*+J, etc.
# Set up a time-stratified analysis:
# 1. Here, un-comment ONLY the files you want to use.
# 2. Also un-comment "BioGeoBEARS_run_object = section_the_tree(...", below.
# 3. For example files see (a) extdata_dir,
# or (b) http://phylo.wikidot.com/biogeobears#files
# and BioGeoBEARS Google Group posts for further hints)
#BioGeoBEARS_run_object$timesfn = np(paste(addslash(extdata_dir), "timeperiods.txt", sep=""))
#BioGeoBEARS_run_object$areas_allowed_fn = np(paste(addslash(extdata_dir), "areas_allowed.txt", sep=""))
#BioGeoBEARS_run_object$areas_adjacency_fn = np(paste(addslash(extdata_dir), "areas_adjacency.txt", sep=""))
#BioGeoBEARS_run_object$distsfn = np(paste(addslash(extdata_dir), "distances_matrix.txt", sep=""))
#BioGeoBEARS_run_object$timesfn = "~/Dropbox (AMNH)/Research/Petaluridae_phylogeny/Divergence_dating/timeperiods.txt"
#BioGeoBEARS_run_object$areas_adjacency_fn = "~/Dropbox (AMNH)/Research/Petaluridae_phylogeny/Divergence_dating/adjacent_areas.txt"
#BioGeoBEARS_run_object$dispersal_multipliers_fn = "~/Dropbox (AMNH)/Research/Petaluridae_phylogeny/Divergence_dating/dispersal_multipliers.txt"
# Speed options and multicore processing if desired
BioGeoBEARS_run_object$on_NaN_error = -1e50 # returns very low lnL if parameters produce NaN error (underflow check)
BioGeoBEARS_run_object$speedup = TRUE # shorcuts to speed ML search; use FALSE if worried (e.g. >3 params)
BioGeoBEARS_run_object$use_optimx = TRUE # if FALSE, use optim() instead of optimx()
BioGeoBEARS_run_object$num_cores_to_use = 6
BioGeoBEARS_run_object$force_sparse = FALSE
BioGeoBEARS_run_object = readfiles_BioGeoBEARS_run(BioGeoBEARS_run_object)
#Divide the tree up by timeperiods/strata (uncomment this for stratified analysis)
#BioGeoBEARS_run_object = section_the_tree(inputs=BioGeoBEARS_run_object, make_master_table=TRUE, plot_pieces=FALSE, cut_fossils=FALSE)
# The stratified tree is described in this table:
#BioGeoBEARS_run_object$master_table
# Good default settings to get ancestral states
BioGeoBEARS_run_object$return_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_TTL_loglike_from_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_ancprobs = TRUE # get ancestral states from optim run
#BioGeoBEARS_run_object$areas_adjacency_fn###RUN DEC#####
# Set up DEC model
# (nothing to do; defaults)
# Look at the BioGeoBEARS_run_object; it's just a list of settings etc.
BioGeoBEARS_run_object
# This contains the model object
BioGeoBEARS_run_object$BioGeoBEARS_model_object
# This table contains the parameters of the model
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table
# Run this to check inputs. Read the error messages if you get them!
BioGeoBEARS_run_object = fix_BioGeoBEARS_params_minmax(BioGeoBEARS_run_object=BioGeoBEARS_run_object)
check_BioGeoBEARS_run(BioGeoBEARS_run_object)
# For a slow analysis, run once, then set runslow=FALSE to just
# load the saved result.
runslow = TRUE
resfn = "Petalurida_DEC_M0_unconstrained_v1.Rdata"
if (runslow)
{
res = bears_optim_run(BioGeoBEARS_run_object)
res
save(res, file=resfn)
resDEC = res
} else {
# Loads to "res"
load(resfn)
resDEC = res
}Run DEC+J
# Get the ML parameter values from the 2-parameter nested model
# (this will ensure that the 3-parameter model always does at least as good)
dstart = resDEC$outputs@params_table["d","est"]
estart = resDEC$outputs@params_table["e","est"]
bstart = resDEC$outputs@params_table["b","est"]
bstart = .5
jstart = 0.0001
resDEC$outputs@params_table
# Input starting values for d, e
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","init"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","est"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","init"] = estart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","est"] = estart
# Add j as a free parameter
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = jstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = jstart
#trying b as a free parameter
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["b","type"] = "free"
#BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["b","init"] = bstart
#BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["b","est"] = bstart
BioGeoBEARS_run_object = fix_BioGeoBEARS_params_minmax(BioGeoBEARS_run_object=BioGeoBEARS_run_object)
check_BioGeoBEARS_run(BioGeoBEARS_run_object)
resfn = "Petaluridae_DEC+J_M0_unconstrained_v1.Rdata"
runslow = TRUE
if (runslow)
{
#sourceall("/Dropbox/_njm/__packages/BioGeoBEARS_setup/")
res = bears_optim_run(BioGeoBEARS_run_object)
res
save(res, file=resfn)
resDECj = res
} else {
# Loads to "res"
load(resfn)
resDECj = res
}
BioGeoBEARS_run_objectPDF plots
pdffn = "Petaluridae_DEC_vs_DEC+J_M0_unconstrained_v1.pdf"
pdf(pdffn, height=6, width=6)Plot ancestral states - DEC
analysis_titletxt ="BioGeoBEARS DEC"
tipranges## An object of class "tipranges"
## numeric(0)
## Slot "df":
## SA EA WA NZ ENA WNA JA
## Petalura_litoreaplate8 0 1 0 0 0 0 0
## Petalura_gigantea 0 1 0 0 0 0 0
## Petalura_hesperia 0 0 1 0 0 0 0
## Petalura_ingentissimaplate8 0 1 0 0 0 0 0
## Uropetala_carovei_filler 0 0 0 1 0 0 0
## Uropetala_chiltoni1plate8 0 0 0 1 0 0 0
## Phenes_raptorplate8 1 0 0 0 0 0 0
## tanypteryx_R 0 0 0 0 0 1 0
## Tanypteryx_pryeriplate8 0 0 0 0 0 0 1
## Tachopteryx_thoreyi20k 0 0 0 0 1 0 0# Setup
results_object = resDEC
scriptdir = np(system.file("extdata/a_scripts", package="BioGeoBEARS"))
# States
pdffn = "~/Desktop/biogeography.pdf"
pdf(pdffn, height=6, width=6)
plot_BioGeoBEARS_results(results_object, plotwhat = "pie")## LnL nparams d e
## 1 -15.13797 2 0.003073225 0.06042132dev.off()## pdf
## 3cmdstr = paste("open ", pdffn, sep="")
system(cmdstr)Plot ancestral states - DEC +J
pdffn = "Petaluridae_DEC+J.pdf"
pdf(pdffn, height=6, width=6)
#######################################################
# Plot ancestral states - DIVALIKE
#######################################################
analysis_titletxt ="BioGeoBEARS DIVALIKE on Petaluridae M0_unconstrained"
analysis_titletxt ="BioGeoBEARS DEC+J on Petaluridae M0_unconstrained"
# Setup
results_object = resDECj
results_object$relative_probs_of_each_state_at_bottom_of_root_branch## [1] 0.01618101 0.01724414 0.01432545 0.01643226 0.01586985 0.01541666
## [7] 0.01541666 0.01671083 0.01525464 0.01630577 0.01609749 0.01585106
## [13] 0.01585106 0.01578506 0.01683619 0.01666785 0.01641019 0.01641019
## [19] 0.01538000 0.01510200 0.01487516 0.01487516 0.01623229 0.01598320
## [25] 0.01598320 0.01564392 0.01564392 0.01541780 0.01591687 0.01661967
## [31] 0.01650915 0.01633630 0.01633630 0.01564605 0.01548969 0.01532973
## [37] 0.01532973 0.01622557 0.01605631 0.01605631 0.01587434 0.01587434
## [43] 0.01571468 0.01600069 0.01586103 0.01569637 0.01569637 0.01659691
## [49] 0.01642296 0.01642296 0.01625768 0.01625768 0.01609332 0.01557745
## [55] 0.01541638 0.01541638 0.01520527 0.01520527 0.01505379 0.01596493
## [61] 0.01596493 0.01580416 0.01556743scriptdir = np(system.file("extdata/a_scripts", package="BioGeoBEARS"))
plot_BioGeoBEARS_results(results_object, plotwhat = "text")## LnL nparams d e b j
## 1 -12.75508 4 0.00689291 0.4786768 0.9999669 4.5599e-05plot_BioGeoBEARS_results(results_object, plotwhat = "pie", plotlegend = T)## LnL nparams d e b j
## 1 -12.75508 4 0.00689291 0.4786768 0.9999669 4.5599e-05dev.off() # Turn off PDF## pdf
## 3cmdstr = paste("open ", pdffn, sep="")
system(cmdstr) # Plot it##DIVALIKE models####
# Set up DIVALIKE model
# Remove subset-sympatry
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","init"] = 0.000001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","est"] = 0.000001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ysv","type"] = "2-j"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ys","type"] = "ysv*1/2"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["y","type"] = "ysv*1/2"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","type"] = "ysv*1/2"
# Allow classic, widespread vicariance; all events equiprobable
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","init"] = 0.5
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","est"] = 0.5
# No jump dispersal/founder-event speciation
# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = 0.01
# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = 0.01
BioGeoBEARS_run_object = fix_BioGeoBEARS_params_minmax(BioGeoBEARS_run_object=BioGeoBEARS_run_object)
check_BioGeoBEARS_run(BioGeoBEARS_run_object)
runslow = TRUE
resfn = "Petaluridae_DIVALIKE_M0_unconstrained_v1.Rdata"
if (runslow)
{
res = bears_optim_run(BioGeoBEARS_run_object)
res
save(res, file=resfn)
resDIVALIKE = res
} else {
# Loads to "res"
load(resfn)
resDIVALIKE = res
}# Set up DIVALIKE+J model
# Get the ML parameter values from the 2-parameter nested model
# (this will ensure that the 3-parameter model always does at least as good)
dstart = resDIVALIKE$outputs@params_table["d","est"]
estart = resDIVALIKE$outputs@params_table["e","est"]
jstart = 0.0001
# Input starting values for d, e
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","init"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","est"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","init"] = estart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","est"] = estart
# Remove subset-sympatry
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","init"] = 0.0000001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","est"] = 0.0000001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ysv","type"] = "2-j"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ys","type"] = "ysv*1/2"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["y","type"] = "ysv*1/2"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","type"] = "ysv*1/2"
# Allow classic, widespread vicariance; all events equiprobable
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","init"] = 0.5
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","est"] = 0.5
# Add jump dispersal/founder-event speciation
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = jstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = jstart
# Under DIVALIKE+J, the max of "j" should be 2, not 3 (as is default in DEC+J)
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","min"] = 0.00001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","max"] = 1.99999
BioGeoBEARS_run_object = fix_BioGeoBEARS_params_minmax(BioGeoBEARS_run_object=BioGeoBEARS_run_object)
check_BioGeoBEARS_run(BioGeoBEARS_run_object)## [1] TRUEresfn = "Petaluridae_DIVALIKE+J_M0_unconstrained_v1.Rdata"
runslow = TRUE
if (runslow)
{
#sourceall("/Dropbox/_njm/__packages/BioGeoBEARS_setup/")
res = bears_optim_run(BioGeoBEARS_run_object)
res
save(res, file=resfn)
resDIVALIKEj = res
} else {
# Loads to "res"
load(resfn)
resDIVALIKEj = res
}## [1] "Note: tipranges_to_tip_condlikes_of_data_on_each_state() is converting a states_list with (0-based) numbers to the equivalent areanames"
##
## Your computer has 8 cores.
##
## Your computer has 8 cores. You have chosen to use:
## num_cores_to_use = 6 cores for the matrix exponentiations in the likelihood calculations.
## Started cluster with 6 cores.
##
## [1] "parscale:"
## [1] 5.00000 5.00000 1.00000 1.99998
##
##
## NOTE: Before running optimx(), here is a test calculation of the data likelihood
## using calc_loglike_for_optim() on initial parameter values, with printlevel=2...
## if this crashes, the error messages are more helpful
## than those from inside optimx().
##
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.698 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.625
##
## calc_loglike_for_optim() on initial parameters loglike=-12.62504
##
##
##
## Calculation of likelihood on initial parameters: successful.
##
## Now starting Maximum Likelihood (ML) parameter optimization with optimx()...
##
##
##
## Printing any warnings() that occurred during calc_loglike_for_optim():
##
## NULL
##
##
## Results of optimx_scalecheck() below. Note: sometimes rescaling parameters may be helpful for ML searches, when the parameters have much different absolute sizes. This can be attempted by setting BioGeoBEARS_run_object$rescale_params = TRUE.
##
## $lpratio
## [1] 4
##
## $lbratio
## [1] 0.69897
##
## Maximizing -- use negfn and neggr
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.698 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.625## Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower, : Parameters or bounds appear to have different scalings.
## This can cause poor performance in optimization.
## It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.## Warning in (function (npt = min(n + 2L, 2L * n), rhobeg = NA, rhoend = NA, :
## unused control arguments ignored## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.698 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.625
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.2 0.698 0 1 0 0 1 0 0.2 1.8 0.9 0.9 0 0.9 0 0 0 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -25.181
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.4 0.698 0 1 0 0 1 0 0.2 1.8 0.9 0.9 0 0.9 0 0 0 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -33.246
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.2 0.898 0 1 0 0 1 0 0.2 1.8 0.9 0.9 0 0.9 0 0 0 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -23.039
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.2 0.698 0 0.8 0 0 1 0 0.2 1.8 0.9 0.9 0 0.9 0 0 0 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -25.181
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.2 0.698 0 1 0 0 1 0 0.4 1.6 0.8 0.8 0 0.8 0 0 0 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -25.181
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0 0.698 0 1 0 0 1 0 0.2 1.8 0.9 0.9 0 0.9 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -14.4
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0 0.898 0 1 0 0 1 0 0.2 1.8 0.9 0.9 0 0.9 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -14.4
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.021 0 1 0 0 1 0 0.357 1.643 0.821 0.821 0 0.821 0 0 0 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.999
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0 0.902 0 1 0 0 1 0 0.1 1.9 0.95 0.95 0 0.95 0 0 0 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -14.471
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.02 0.878 0 0.98 0 0 1 0 0.2 1.8 0.9 0.9 0 0.9 0 0 0 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -15.578
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0 0.852 0 1 0 0 1 0 0.221 1.779 0.89 0.89 0 0.89 0 0 0 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -14.462
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.02 0.898 0 1 0 0 1 0 0.2 1.8 0.9 0.9 0 0.9 0 0 0 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -15.582
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0 0.905 0 0.982 0 0 1 0 0.198 1.802 0.901 0.901 0 0.901 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.395
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.891 0 0.968 0 0 1 0 0.201 1.799 0.9 0.9 0 0.9 0 0 0 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.402
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.913 0 0.98 0 0 1 0 0.192 1.808 0.904 0.904 0 0.904 0 0 0 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.38
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.93 0 0.976 0 0 1 0 0.183 1.817 0.909 0.909 0 0.909 0 0 0 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.358
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.961 0 0.963 0 0 1 0 0.161 1.839 0.92 0.92 0 0.92 0 0 0 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.324
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.01 0 0.914 0 0 1 0 0.121 1.879 0.94 0.94 0 0.94 0 0 0 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.361
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.017 0.954 0 0.956 0 0 1 0 0.154 1.846 0.923 0.923 0 0.923 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -15.085
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0 0.943 0 0.927 0 0 1 0 0.157 1.843 0.921 0.921 0 0.921 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.321
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.947 0 0.924 0 0 1 0 0.165 1.835 0.917 0.917 0 0.917 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.156
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0 0.956 0 0.918 0 0 1 0 0.182 1.818 0.909 0.909 0 0.909 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.356
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.941 0 0.925 0 0 1 0 0.17 1.83 0.915 0.915 0 0.915 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.201
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.013 0.949 0 0.924 0 0 1 0 0.164 1.836 0.918 0.918 0 0.918 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.831
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.949 0 0.928 0 0 1 0 0.166 1.834 0.917 0.917 0 0.917 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.162
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.95 0 0.923 0 0 1 0 0.167 1.833 0.916 0.916 0 0.916 0 0 0 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.331
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.946 0 0.925 0 0 1 0 0.164 1.836 0.918 0.918 0 0.918 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.132
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.945 0 0.924 0 0 1 0 0.163 1.837 0.918 0.918 0 0.918 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.131
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.945 0 0.926 0 0 1 0 0.163 1.837 0.918 0.918 0 0.918 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.133
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.945 0 0.923 0 0 1 0 0.163 1.837 0.918 0.918 0 0.918 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.126
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.945 0 0.921 0 0 1 0 0.163 1.837 0.919 0.919 0 0.919 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.127
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.945 0 0.923 0 0 1 0 0.164 1.836 0.918 0.918 0 0.918 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.131
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.946 0 0.923 0 0 1 0 0.162 1.838 0.919 0.919 0 0.919 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.123
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.947 0 0.924 0 0 1 0 0.162 1.838 0.919 0.919 0 0.919 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.126
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.946 0 0.923 0 0 1 0 0.163 1.837 0.919 0.919 0 0.919 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.123
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.946 0 0.923 0 0 1 0 0.162 1.838 0.919 0.919 0 0.919 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.122
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.946 0 0.922 0 0 1 0 0.162 1.838 0.919 0.919 0 0.919 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.119
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.946 0 0.921 0 0 1 0 0.161 1.839 0.919 0.919 0 0.919 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.115
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.002 0.947 0 0.92 0 0 1 0 0.16 1.84 0.92 0.92 0 0.92 0 0 0 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.11
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.947 0 0.92 0 0 1 0 0.159 1.841 0.921 0.921 0 0.921 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.106
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.948 0 0.919 0 0 1 0 0.158 1.842 0.921 0.921 0 0.921 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.097
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.949 0 0.917 0 0 1 0 0.156 1.844 0.922 0.922 0 0.922 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.085
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.951 0 0.913 0 0 1 0 0.151 1.849 0.924 0.924 0 0.924 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.062
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.956 0 0.906 0 0 1 0 0.143 1.857 0.929 0.929 0 0.929 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.018
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.963 0 0.891 0 0 1 0 0.125 1.875 0.937 0.937 0 0.937 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.957
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.981 0 0.863 0 0 1 0 0.09 1.91 0.955 0.955 0 0.955 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.879
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.989 0 0.849 0 0 1 0 0.074 1.926 0.963 0.963 0 0.963 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.88
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 0.978 0 0.866 0 0 1 0 0.087 1.913 0.957 0.957 0 0.957 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.916
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 0.979 0 0.865 0 0 1 0 0.088 1.912 0.956 0.956 0 0.956 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.659
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.001 0.971 0 0.866 0 0 1 0 0.081 1.919 0.96 0.96 0 0.96 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.277
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.979 0 0.87 0 0 1 0 0.09 1.91 0.955 0.955 0 0.955 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.666
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.983 0 0.867 0 0 1 0 0.084 1.916 0.958 0.958 0 0.958 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.624
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.006 0.984 0 0.862 0 0 1 0 0.08 1.92 0.96 0.96 0 0.96 0 0 0 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.6
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.986 0 0.86 0 0 1 0 0.077 1.923 0.961 0.961 0 0.961 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.58
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.986 0 0.861 0 0 1 0 0.077 1.923 0.961 0.961 0 0.961 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.578
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.987 0 0.861 0 0 1 0 0.077 1.923 0.962 0.962 0 0.962 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.576
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.987 0 0.861 0 0 1 0 0.077 1.923 0.962 0.962 0 0.962 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.576
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.987 0 0.861 0 0 1 0 0.077 1.923 0.962 0.962 0 0.962 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.576
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.987 0 0.861 0 0 1 0 0.077 1.923 0.962 0.962 0 0.962 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.575
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.987 0 0.861 0 0 1 0 0.077 1.923 0.962 0.962 0 0.962 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.575
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.987 0 0.861 0 0 1 0 0.077 1.923 0.962 0.962 0 0.962 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.574
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 0.987 0 0.861 0 0 1 0 0.076 1.924 0.962 0.962 0 0.962 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.57
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 0.987 0 0.861 0 0 1 0 0.076 1.924 0.962 0.962 0 0.962 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.565
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 0.988 0 0.86 0 0 1 0 0.075 1.925 0.963 0.963 0 0.963 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.556
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 0.989 0 0.858 0 0 1 0 0.072 1.928 0.964 0.964 0 0.964 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.539
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 0.992 0 0.855 0 0 1 0 0.067 1.933 0.966 0.966 0 0.966 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.504
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 0.999 0 0.849 0 0 1 0 0.059 1.941 0.971 0.971 0 0.971 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.443
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.006 1.009 0 0.835 0 0 1 0 0.04 1.96 0.98 0.98 0 0.98 0 0 0 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.338
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.032 0 0.81 0 0 1 0 0.001 1.999 0.999 0.999 0 0.999 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.514
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 1.012 0 0.833 0 0 1 0 0.043 1.957 0.979 0.979 0 0.979 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.465
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.001 0 0.836 0 0 1 0 0.033 1.967 0.983 0.983 0 0.983 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.229
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.014 1.004 0 0.825 0 0 1 0 0.035 1.965 0.983 0.983 0 0.983 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.447
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.004 0 0.836 0 0 1 0 0.029 1.971 0.985 0.985 0 0.985 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.214
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.01 1.008 0 0.838 0 0 1 0 0.032 1.968 0.984 0.984 0 0.984 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.233
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.004 0 0.835 0 0 1 0 0.026 1.974 0.987 0.987 0 0.987 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.192
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.006 0 0.832 0 0 1 0 0.026 1.974 0.987 0.987 0 0.987 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.212
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.004 0 0.834 0 0 1 0 0.027 1.973 0.986 0.986 0 0.986 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.179
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.005 0 0.834 0 0 1 0 0.026 1.974 0.987 0.987 0 0.987 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.16
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.005 0 0.833 0 0 1 0 0.025 1.975 0.987 0.987 0 0.987 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.147
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.007 0 0.832 0 0 1 0 0.022 1.978 0.989 0.989 0 0.989 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.121
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.008 0 0.829 0 0 1 0 0.017 1.983 0.992 0.992 0 0.992 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.082
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.012 0 0.83 0 0 1 0 0.012 1.988 0.994 0.994 0 0.994 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.07
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.011 0 0.825 0 0 1 0 0.008 1.992 0.996 0.996 0 0.996 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.037
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.013 0 0.822 0 0 1 0 0.003 1.997 0.999 0.999 0 0.999 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.05
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.013 0 0.824 0 0 1 0 0.009 1.991 0.995 0.995 0 0.995 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.988
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.014 0 0.822 0 0 1 0 0.011 1.989 0.994 0.994 0 0.994 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.018
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.012 0 0.824 0 0 1 0 0.009 1.991 0.995 0.995 0 0.995 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.994
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.013 0 0.824 0 0 1 0 0.01 1.99 0.995 0.995 0 0.995 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.997
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.013 0 0.824 0 0 1 0 0.008 1.992 0.996 0.996 0 0.996 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.982
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.013 0 0.823 0 0 1 0 0.008 1.992 0.996 0.996 0 0.996 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.979
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.013 0 0.824 0 0 1 0 0.008 1.992 0.996 0.996 0 0.996 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.972
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.014 0 0.825 0 0 1 0 0.007 1.993 0.997 0.997 0 0.997 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.957
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.015 0 0.827 0 0 1 0 0.005 1.995 0.998 0.998 0 0.998 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.926
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.018 0 0.831 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.87
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.019 0 0.832 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.866
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.019 0 0.832 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.866
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.019 0 0.832 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.878
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.019 0 0.832 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.858
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.018 0 0.832 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.852
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.019 0 0.832 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.854
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.018 0 0.832 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.856
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.018 0 0.832 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.852
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.018 0 0.832 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.852
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.019 0 0.832 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.851
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.019 0 0.833 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.85
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.019 0 0.834 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.848
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.02 0 0.835 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.845
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.02 0 0.836 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.842
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.021 0 0.839 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.836
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.023 0 0.844 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.823
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.027 0 0.854 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.804
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.034 0 0.876 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.752
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.05 0 0.917 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.671
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.005 1.079 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.665
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 1.079 0 1 0 0 1 0 0.018 1.982 0.991 0.991 0 0.991 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.795
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 1.063 0 0.969 0 0 1 0 0.028 1.972 0.986 0.986 0 0.986 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.939
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.023 1.076 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -14.098
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.099 0 0.993 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.664
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.011 1.103 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.664
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.012 1.091 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.825
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.099 0 0.993 0 0 1 0 0.003 1.997 0.999 0.999 0 0.999 0 0 0
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.727
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.105 0 0.992 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.723
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.099 0 0.993 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.528
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.098 0 0.994 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.535
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.1 0 0.994 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.528
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.101 0 0.994 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.513
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.101 0 0.995 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.512
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.102 0 0.994 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.51
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.102 0 0.994 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.511
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.102 0 0.994 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.516
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.102 0 0.995 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.51
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.102 0 0.995 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.509
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.103 0 0.996 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.507
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.104 0 0.998 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.505
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.104 0 0.999 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.504
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.503
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.503
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.503
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.512
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.515
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.504
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.504
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.502
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.215 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.482
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.994 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.524
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.16 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.491
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.05 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.512
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.133 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.496
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.077 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.506
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.119 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.498
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.091 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.503
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 1.1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.443
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.9 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.787
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 1.05 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.448
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.95 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.611
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 1.025 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.468
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.975 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.548
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 1.012 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.482
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.987 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.522
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.502
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.499
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.502
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.5
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.5
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.5
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.215 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.491
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.994 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.535
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.16 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.493
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.05 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.514
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.133 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.496
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.077 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.507
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.119 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.498
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.091 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.503
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.105 0 1.1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.515
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.9 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.884
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.105 0 1.05 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.467
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.95 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.633
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.105 0 1.025 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.473
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.975 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.553
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 1.105 0 1.012 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.484
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.987 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.524
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.215 0 1.1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.424
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.994 0 0.9 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.81
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.16 0 1.05 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.438
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.05 0 0.95 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.621
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.133 0 1.025 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.463
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.077 0 0.975 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.553
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.119 0 1.012 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.48
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.091 0 0.987 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.525
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.514
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.514
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.505
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.503
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.502
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.215 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.484
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.994 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.522
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.16 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.492
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.05 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.511
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.133 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.496
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.077 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.506
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.119 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.498
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.091 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.503
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 1.1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.446
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.9 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.786
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 1.05 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.449
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.95 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.61
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 1.025 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.468
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.975 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.548
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 1.012 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.483
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 1.105 0 0.987 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.522
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.502
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.499
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.5
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.5
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.501
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 1.105 0 1 0 0 1 0 0 2 1 1 0 1 0 0 0 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.5
##
##
## This is the output from optim, optimx, or GenSA. Check the help on those functions to
## interpret this output and check for convergence issues:
##
## p1 p2 p3 p4 value fevals gevals niter convcode
## bobyqa 0.007455278 1.10488 1 1e-05 -12.50069 162 NA NA 0
## kkt1 kkt2 xtime
## bobyqa FALSE TRUE 3.122
##
##
## Stopping cluster with 6 cores.pdffn = "Petaluridae_DIVALIKE+J.pdf"
pdf(pdffn, height=6, width=6)
#######################################################
# Plot ancestral states - DIVALIKE
#######################################################
analysis_titletxt ="BioGeoBEARS DIVALIKE on Petaluridae M0_unconstrained"
analysis_titletxt ="BioGeoBEARS DEC+J on Petaluridae M0_unconstrained"
# Setup
results_object = resDIVALIKEj
results_object## $computed_likelihoods_at_each_node
## [1] 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000
## [7] 1.00000000 1.00000000 1.00000000 1.00000000 0.01491220 0.13908281
## [13] 0.26643791 0.03639711 1.09672264 1.25477368 1.03439699 0.10442463
## [19] 1.24562825
##
## $relative_probs_of_each_state_at_branch_top_AT_node_DOWNPASS
## [,1] [,2] [,3] [,4] [,5]
## [1,] 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
## [7,] 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0160776840 0.0169643953 0.0146934722 0.0163026355 0.0158561489
## [12,] 0.0177356929 0.0203679066 0.0136372442 0.0184065524 0.0134665780
## [13,] 0.0134031289 0.0229165714 0.0136383916 0.0202103388 0.0134031289
## [14,] 0.0007076999 0.2880845781 0.0073442097 0.0007076999 0.0007076999
## [15,] 0.0014928160 0.4951949165 0.0014928160 0.0014928160 0.0014928160
## [16,] 0.0016435551 0.0255965024 0.0255965024 0.0016435551 0.0016435551
## [17,] 0.0003865795 0.0003865795 0.0003865795 0.7145740721 0.0003865795
## [18,] 0.0091893492 0.0091893492 0.0091893492 0.0091893492 0.0256288105
## [19,] 0.0038617847 0.0038617847 0.0038617847 0.0038617847 0.0038617847
## [,6] [,7] [,8] [,9] [,10]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0155250212 0.0155250212 0.0165210616 0.0153855610 0.0161901700
## [12,] 0.0134665780 0.0134665780 0.0201459000 0.0157135090 0.0188542752
## [13,] 0.0134031289 0.0134031289 0.0181599223 0.0135206820 0.0168067587
## [14,] 0.0007076999 0.0007076999 0.0175494808 0.0040252351 0.0007075017
## [15,] 0.0014928160 0.0014928160 0.0271851142 0.0014925622 0.0014925622
## [16,] 0.0016435551 0.0016435551 0.0136193330 0.0136193330 0.0016433182
## [17,] 0.0003865795 0.0003865795 0.0003864214 0.0003864214 0.0166140833
## [18,] 0.0211843749 0.0211843749 0.0091891479 0.0091891479 0.0091891479
## [19,] 0.0313802772 0.0313802772 0.0038615115 0.0038615115 0.0038615115
## [,11] [,12] [,13] [,14] [,15]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [11,] 0.0160270272 0.0158451473 0.0158451473 0.0158289318 0.016633541
## [12,] 0.0156011187 0.0156011187 0.0156011187 0.0170026127 0.019387346
## [13,] 0.0134030468 0.0134030468 0.0134030468 0.0182775567 0.023979680
## [14,] 0.0007075017 0.0007075017 0.0007075017 0.1477212410 0.017549481
## [15,] 0.0014925622 0.0014925622 0.0014925622 0.0271851142 0.027185114
## [16,] 0.0016433182 0.0016433182 0.0016433182 0.2001527996 0.013619333
## [17,] 0.0003864214 0.0003864214 0.0003864214 0.0003864214 0.016614083
## [18,] 0.0174090581 0.0151868158 0.0151868158 0.0091891479 0.009189148
## [19,] 0.0038615115 0.0176207454 0.0176207454 0.0038615115 0.003861511
## [,16] [,17] [,18] [,19] [,20]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [11,] 0.0165073667 0.0163154541 0.0163154541 0.015498041 0.0152771901
## [12,] 0.0169172766 0.0169172766 0.0169172766 0.016021903 0.0135518328
## [13,] 0.0181599223 0.0181599223 0.0181599223 0.016984141 0.0135206820
## [14,] 0.0175494808 0.0175494808 0.0175494808 0.004025235 0.0040252351
## [15,] 0.0271851142 0.0271851142 0.0271851142 0.001492562 0.0014925622
## [16,] 0.0136193330 0.0136193330 0.0136193330 0.013619333 0.0136193330
## [17,] 0.0003864214 0.0003864214 0.0003864214 0.016614083 0.0003864214
## [18,] 0.0174090581 0.0151868158 0.0151868158 0.009189148 0.0174090581
## [19,] 0.0038615115 0.0176207454 0.0176207454 0.003861511 0.0038615115
## [,21] [,22] [,23] [,24] [,25]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0151109695 0.0151109695 0.0161488852 0.0159644603 0.0159644603
## [12,] 0.0135518328 0.0135518328 0.0159365669 0.0159365669 0.0159365669
## [13,] 0.0135206820 0.0135206820 0.0168067587 0.0168067587 0.0168067587
## [14,] 0.0040252351 0.0040252351 0.0007075017 0.0007075017 0.0007075017
## [15,] 0.0014925622 0.0014925622 0.0014925622 0.0014925622 0.0014925622
## [16,] 0.0136193330 0.0136193330 0.0016433182 0.0016433182 0.0016433182
## [17,] 0.0003864214 0.0003864214 0.0166140833 0.0166140833 0.0166140833
## [18,] 0.0151868158 0.0151868158 0.0174090581 0.0151868158 0.0151868158
## [19,] 0.0176207454 0.0176207454 0.0038615115 0.0176207454 0.0176207454
## [,26] [,27] [,28] [,29] [,30]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.000000000
## [11,] 0.0156905772 0.0156905772 0.0155250085 0.0159118088 0.016447251
## [12,] 0.0134664968 0.0134664968 0.0134664968 0.0176171339 0.019455225
## [13,] 0.0134030468 0.0134030468 0.0134030468 0.0166515237 0.019640978
## [14,] 0.0007075017 0.0007075017 0.0007075017 0.0563534508 0.011993094
## [15,] 0.0014925622 0.0014925622 0.0014925622 0.0186817499 0.018681750
## [16,] 0.0016433182 0.0016433182 0.0016433182 0.0756260954 0.009655983
## [17,] 0.0003864214 0.0003864214 0.0003864214 0.0003949938 0.011315050
## [18,] 0.0341369484 0.0341369484 0.0211844842 0.0091998358 0.009199836
## [19,] 0.0176207454 0.0176207454 0.1294341422 0.0038760574 0.003876057
## [,31] [,32] [,33] [,34] [,35]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [11,] 0.0163509025 0.0162265513 0.0162265513 0.015691611 0.0155638205
## [12,] 0.0175513590 0.0175513590 0.0175513590 0.016861228 0.0149573621
## [13,] 0.0165732342 0.0165732342 0.0165732342 0.015770936 0.0134857143
## [14,] 0.0119930941 0.0119930941 0.0119930941 0.002948312 0.0029483123
## [15,] 0.0186817499 0.0186817499 0.0186817499 0.001506141 0.0015061410
## [16,] 0.0096559832 0.0096559832 0.0096559832 0.009655983 0.0096559832
## [17,] 0.0003949938 0.0003949938 0.0003949938 0.011315050 0.0003949938
## [18,] 0.0146734204 0.0131927751 0.0131927751 0.009199836 0.0146734204
## [19,] 0.0038760574 0.0130491932 0.0130491932 0.003876057 0.0038760574
## [,36] [,37] [,38] [,39] [,40]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0154480011 0.0154480011 0.0161215421 0.0159996773 0.0159996773
## [12,] 0.0149573621 0.0149573621 0.0167954532 0.0167954532 0.0167954532
## [13,] 0.0134857143 0.0134857143 0.0156728042 0.0156728042 0.0156728042
## [14,] 0.0029483123 0.0029483123 0.0007181557 0.0007181557 0.0007181557
## [15,] 0.0015061410 0.0015061410 0.0015061410 0.0015061410 0.0015061410
## [16,] 0.0096559832 0.0096559832 0.0016559766 0.0016559766 0.0016559766
## [17,] 0.0003949938 0.0003949938 0.0113150503 0.0113150503 0.0113150503
## [18,] 0.0131927751 0.0131927751 0.0146734204 0.0131927751 0.0131927751
## [19,] 0.0130491932 0.0130491932 0.0038760574 0.0130491932 0.0130491932
## [,41] [,42] [,43] [,44] [,45]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.0000000000
## [11,] 0.0158542763 0.0158542763 0.0157386734 0.015986661 0.0158711476
## [12,] 0.0148915872 0.0148915872 0.0148915872 0.017467854 0.0158240494
## [13,] 0.0134074248 0.0134074248 0.0134074248 0.019739109 0.0166515237
## [14,] 0.0007181557 0.0007181557 0.0007181557 0.056353451 0.0563534508
## [15,] 0.0015061410 0.0015061410 0.0015061410 0.018681750 0.0186817499
## [16,] 0.0016559766 0.0016559766 0.0016559766 0.075626095 0.0756260954
## [17,] 0.0003949938 0.0003949938 0.0003949938 0.011315050 0.0003949938
## [18,] 0.0222298412 0.0222298412 0.0171857149 0.009199836 0.0146734204
## [19,] 0.0130491932 0.0130491932 0.0547858746 0.003876057 0.0038760574
## [,46] [,47] [,48] [,49] [,50]
## [1,] 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## [2,] 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## [3,] 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## [4,] 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## [5,] 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## [6,] 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## [7,] 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## [8,] 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## [9,] 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## [10,] 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## [11,] 0.0157519966 0.0157519966 0.016428870 0.016303673 0.016303673
## [12,] 0.0158240494 0.0158240494 0.017411064 0.017411064 0.017411064
## [13,] 0.0166515237 0.0166515237 0.019640978 0.019640978 0.019640978
## [14,] 0.0563534508 0.0563534508 0.011993094 0.011993094 0.011993094
## [15,] 0.0186817499 0.0186817499 0.018681750 0.018681750 0.018681750
## [16,] 0.0756260954 0.0756260954 0.009655983 0.009655983 0.009655983
## [17,] 0.0003949938 0.0003949938 0.011315050 0.011315050 0.011315050
## [18,] 0.0131927751 0.0131927751 0.014673420 0.013192775 0.013192775
## [19,] 0.0130491932 0.0130491932 0.003876057 0.013049193 0.013049193
## [,51] [,52] [,53] [,54] [,55]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## [11,] 0.0161705488 0.0161705488 0.0160516145 0.015641787 0.015525123
## [12,] 0.0157672592 0.0157672592 0.0157672592 0.015171399 0.015171399
## [13,] 0.0165732342 0.0165732342 0.0165732342 0.015770936 0.015770936
## [14,] 0.0119930941 0.0119930941 0.0119930941 0.002948312 0.002948312
## [15,] 0.0186817499 0.0186817499 0.0186817499 0.001506141 0.001506141
## [16,] 0.0096559832 0.0096559832 0.0096559832 0.009655983 0.009655983
## [17,] 0.0003949938 0.0003949938 0.0003949938 0.011315050 0.011315050
## [18,] 0.0222298412 0.0222298412 0.0171857149 0.014673420 0.013192775
## [19,] 0.0130491932 0.0130491932 0.0547858746 0.003876057 0.013049193
## [,56] [,57] [,58] [,59] [,60]
## [1,] 0.000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.015525123 0.0153605561 0.0153605561 0.0152501535 0.0159345117
## [12,] 0.015171399 0.0135275935 0.0135275935 0.0135275935 0.0151146083
## [13,] 0.015770936 0.0134857143 0.0134857143 0.0134857143 0.0156728042
## [14,] 0.002948312 0.0029483123 0.0029483123 0.0029483123 0.0007181557
## [15,] 0.001506141 0.0015061410 0.0015061410 0.0015061410 0.0015061410
## [16,] 0.009655983 0.0096559832 0.0096559832 0.0096559832 0.0016559766
## [17,] 0.011315050 0.0003949938 0.0003949938 0.0003949938 0.0113150503
## [18,] 0.013192775 0.0222298412 0.0222298412 0.0171857149 0.0222298412
## [19,] 0.013049193 0.0130491932 0.0130491932 0.0547858746 0.0130491932
## [,61] [,62] [,63]
## [1,] 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0159345117 0.0158180629 0.0156358863
## [12,] 0.0151146083 0.0151146083 0.0134708033
## [13,] 0.0156728042 0.0156728042 0.0134074248
## [14,] 0.0007181557 0.0007181557 0.0007181557
## [15,] 0.0015061410 0.0015061410 0.0015061410
## [16,] 0.0016559766 0.0016559766 0.0016559766
## [17,] 0.0113150503 0.0113150503 0.0003949938
## [18,] 0.0222298412 0.0171857149 0.0297862608
## [19,] 0.0130491932 0.0547858746 0.0547858746
##
## $condlikes_of_each_state
## [,1] [,2] [,3] [,4] [,5]
## [1,] 0.000000e+00 1.0000000000 0.0000000000 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 1.0000000000 0.0000000000 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.0000000000 1.0000000000 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 1.0000000000 0.0000000000 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.0000000000 0.0000000000 1.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.0000000000 0.0000000000 1.000000e+00 0.000000e+00
## [7,] 1.000000e+00 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00 1.000000e+00
## [9,] 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00
## [11,] 2.397536e-04 0.0002529765 0.0002191120 2.431082e-04 2.364501e-04
## [12,] 2.466730e-03 0.0028328258 0.0018967063 2.560035e-03 1.872970e-03
## [13,] 3.571102e-03 0.0061058435 0.0036337846 5.384800e-03 3.571102e-03
## [14,] 2.575823e-05 0.0104854470 0.0002673080 2.575823e-05 2.575823e-05
## [15,] 1.637205e-03 0.5430914760 0.0016372051 1.637205e-03 1.637205e-03
## [16,] 2.062290e-03 0.0321178176 0.0321178176 2.062290e-03 2.062290e-03
## [17,] 3.998767e-04 0.0003998767 0.0003998767 7.391533e-01 3.998767e-04
## [18,] 9.595944e-04 0.0009595944 0.0009595944 9.595944e-04 2.676279e-03
## [19,] 4.810348e-03 0.0048103482 0.0048103482 4.810348e-03 4.810348e-03
## [,6] [,7] [,8] [,9] [,10]
## [1,] 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00
## [9,] 0.000000e+00 1.000000e+00 0.0000000000 0.0000000000 0.000000e+00
## [10,] 1.000000e+00 0.000000e+00 0.0000000000 0.0000000000 0.000000e+00
## [11,] 2.315122e-04 2.315122e-04 0.0002463654 0.0002294326 2.414311e-04
## [12,] 1.872970e-03 1.872970e-03 0.0028019485 0.0021854790 2.622306e-03
## [13,] 3.571102e-03 3.571102e-03 0.0048384918 0.0036024223 4.477958e-03
## [14,] 2.575823e-05 2.575823e-05 0.0006387504 0.0001465069 2.575102e-05
## [15,] 1.637205e-03 1.637205e-03 0.0298145302 0.0016369268 1.636927e-03
## [16,] 2.062290e-03 2.062290e-03 0.0170891806 0.0170891806 2.061992e-03
## [17,] 3.998767e-04 3.998767e-04 0.0003997131 0.0003997131 1.718556e-02
## [18,] 2.212171e-03 2.212171e-03 0.0009595734 0.0009595734 9.595734e-04
## [19,] 3.908816e-02 3.908816e-02 0.0048100078 0.0048100078 4.810008e-03
## [,11] [,12] [,13] [,14] [,15]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [11,] 2.389982e-04 2.362860e-04 2.362860e-04 0.0002360442 0.0002480427
## [12,] 2.169847e-03 2.169847e-03 2.169847e-03 0.0023647712 0.0026964466
## [13,] 3.571080e-03 3.571080e-03 3.571080e-03 0.0048698341 0.0063890959
## [14,] 2.575102e-05 2.575102e-05 2.575102e-05 0.0053766267 0.0006387504
## [15,] 1.636927e-03 1.636927e-03 1.636927e-03 0.0298145302 0.0298145302
## [16,] 2.061992e-03 2.061992e-03 2.061992e-03 0.2511464655 0.0170891806
## [17,] 3.997131e-04 3.997131e-04 3.997131e-04 0.0003997131 0.0171855576
## [18,] 1.817934e-03 1.585878e-03 1.585878e-03 0.0009595734 0.0009595734
## [19,] 4.810008e-03 2.194890e-02 2.194890e-02 0.0048100078 0.0048100078
## [,16] [,17] [,18] [,19] [,20]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0002461612 0.0002432993 0.0002432993 0.0002311099 0.0002278165
## [12,] 0.0023529024 0.0023529024 0.0023529024 0.0022283713 0.0018848270
## [13,] 0.0048384918 0.0048384918 0.0048384918 0.0045252191 0.0036024223
## [14,] 0.0006387504 0.0006387504 0.0006387504 0.0001465069 0.0001465069
## [15,] 0.0298145302 0.0298145302 0.0298145302 0.0016369268 0.0016369268
## [16,] 0.0170891806 0.0170891806 0.0170891806 0.0170891806 0.0170891806
## [17,] 0.0003997131 0.0003997131 0.0003997131 0.0171855576 0.0003997131
## [18,] 0.0018179344 0.0015858776 0.0015858776 0.0009595734 0.0018179344
## [19,] 0.0048100078 0.0219488982 0.0219488982 0.0048100078 0.0048100078
## [,21] [,22] [,23] [,24] [,25]
## [1,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 0.0002253378 0.0002253378 2.408154e-04 2.380652e-04 2.380652e-04
## [12,] 0.0018848270 0.0018848270 2.216503e-03 2.216503e-03 2.216503e-03
## [13,] 0.0036024223 0.0036024223 4.477958e-03 4.477958e-03 4.477958e-03
## [14,] 0.0001465069 0.0001465069 2.575102e-05 2.575102e-05 2.575102e-05
## [15,] 0.0016369268 0.0016369268 1.636927e-03 1.636927e-03 1.636927e-03
## [16,] 0.0170891806 0.0170891806 2.061992e-03 2.061992e-03 2.061992e-03
## [17,] 0.0003997131 0.0003997131 1.718556e-02 1.718556e-02 1.718556e-02
## [18,] 0.0015858776 0.0015858776 1.817934e-03 1.585878e-03 1.585878e-03
## [19,] 0.0219488982 0.0219488982 4.810008e-03 2.194890e-02 2.194890e-02
## [,26] [,27] [,28] [,29] [,30]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000 0.0000000000
## [11,] 2.339810e-04 2.339810e-04 2.315120e-04 0.0002372801 0.0002452647
## [12,] 1.872958e-03 1.872958e-03 1.872958e-03 0.0024502405 0.0027058874
## [13,] 3.571080e-03 3.571080e-03 3.571080e-03 0.0044365972 0.0052331011
## [14,] 2.575102e-05 2.575102e-05 2.575102e-05 0.0020511029 0.0004365140
## [15,] 1.636927e-03 1.636927e-03 1.636927e-03 0.0204886980 0.0204886980
## [16,] 2.061992e-03 2.061992e-03 2.061992e-03 0.0948936343 0.0121160736
## [17,] 3.997131e-04 3.997131e-04 3.997131e-04 0.0004085804 0.0117042540
## [18,] 3.564738e-03 3.564738e-03 2.212182e-03 0.0009606894 0.0009606894
## [19,] 2.194890e-02 2.194890e-02 1.612268e-01 0.0048281266 0.0048281266
## [,31] [,32] [,33] [,34] [,35]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0002438279 0.0002419736 0.0002419736 0.0002339964 0.0002320908
## [12,] 0.0024410924 0.0024410924 0.0024410924 0.0023451070 0.0020803120
## [13,] 0.0044157379 0.0044157379 0.0044157379 0.0042019752 0.0035931056
## [14,] 0.0004365140 0.0004365140 0.0004365140 0.0001073101 0.0001073101
## [15,] 0.0204886980 0.0204886980 0.0204886980 0.0016518190 0.0016518190
## [16,] 0.0121160736 0.0121160736 0.0121160736 0.0121160736 0.0121160736
## [17,] 0.0004085804 0.0004085804 0.0004085804 0.0117042540 0.0004085804
## [18,] 0.0015322665 0.0013776507 0.0013776507 0.0009606894 0.0015322665
## [19,] 0.0048281266 0.0162544437 0.0162544437 0.0048281266 0.0048281266
## [,36] [,37] [,38] [,39] [,40]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0002303637 0.0002303637 0.0002404077 0.0002385904 0.0002385904
## [12,] 0.0020803120 0.0020803120 0.0023359589 0.0023359589 0.0023359589
## [13,] 0.0035931056 0.0035931056 0.0041758292 0.0041758292 0.0041758292
## [14,] 0.0001073101 0.0001073101 0.0000261388 0.0000261388 0.0000261388
## [15,] 0.0016518190 0.0016518190 0.0016518190 0.0016518190 0.0016518190
## [16,] 0.0121160736 0.0121160736 0.0020778759 0.0020778759 0.0020778759
## [17,] 0.0004085804 0.0004085804 0.0117042540 0.0117042540 0.0117042540
## [18,] 0.0013776507 0.0013776507 0.0015322665 0.0013776507 0.0013776507
## [19,] 0.0162544437 0.0162544437 0.0048281266 0.0162544437 0.0162544437
## [,41] [,42] [,43] [,44] [,45]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0002364221 0.0002364221 0.0002346983 0.0002383963 0.0002366737
## [12,] 0.0020711638 0.0020711638 0.0020711638 0.0024294783 0.0022008533
## [13,] 0.0035722463 0.0035722463 0.0035722463 0.0052592470 0.0044365972
## [14,] 0.0000261388 0.0000261388 0.0000261388 0.0020511029 0.0020511029
## [15,] 0.0016518190 0.0016518190 0.0016518190 0.0204886980 0.0204886980
## [16,] 0.0020778759 0.0020778759 0.0020778759 0.0948936343 0.0948936343
## [17,] 0.0004085804 0.0004085804 0.0004085804 0.0117042540 0.0004085804
## [18,] 0.0023213429 0.0023213429 0.0017946119 0.0009606894 0.0015322665
## [19,] 0.0162544437 0.0162544437 0.0682428330 0.0048281266 0.0048281266
## [,46] [,47] [,48] [,49] [,50]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0002348969 0.0002348969 0.0002449906 0.0002431236 0.0002431236
## [12,] 0.0022008533 0.0022008533 0.0024215798 0.0024215798 0.0024215798
## [13,] 0.0044365972 0.0044365972 0.0052331011 0.0052331011 0.0052331011
## [14,] 0.0020511029 0.0020511029 0.0004365140 0.0004365140 0.0004365140
## [15,] 0.0204886980 0.0204886980 0.0204886980 0.0204886980 0.0204886980
## [16,] 0.0948936343 0.0948936343 0.0121160736 0.0121160736 0.0121160736
## [17,] 0.0004085804 0.0004085804 0.0117042540 0.0117042540 0.0117042540
## [18,] 0.0013776507 0.0013776507 0.0015322665 0.0013776507 0.0013776507
## [19,] 0.0162544437 0.0162544437 0.0048281266 0.0162544437 0.0162544437
## [,51] [,52] [,53] [,54] [,55]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0002411385 0.0002411385 0.0002393649 0.0002332535 0.0002315137
## [12,] 0.0021929548 0.0021929548 0.0021929548 0.0021100808 0.0021100808
## [13,] 0.0044157379 0.0044157379 0.0044157379 0.0042019752 0.0042019752
## [14,] 0.0004365140 0.0004365140 0.0004365140 0.0001073101 0.0001073101
## [15,] 0.0204886980 0.0204886980 0.0204886980 0.0016518190 0.0016518190
## [16,] 0.0121160736 0.0121160736 0.0121160736 0.0121160736 0.0121160736
## [17,] 0.0004085804 0.0004085804 0.0004085804 0.0117042540 0.0117042540
## [18,] 0.0023213429 0.0023213429 0.0017946119 0.0015322665 0.0013776507
## [19,] 0.0162544437 0.0162544437 0.0682428330 0.0048281266 0.0162544437
## [,56] [,57] [,58] [,59] [,60]
## [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0002315137 0.0002290597 0.0002290597 0.0002274133 0.0002376186
## [12,] 0.0021100808 0.0018814558 0.0018814558 0.0018814558 0.0021021822
## [13,] 0.0042019752 0.0035931056 0.0035931056 0.0035931056 0.0041758292
## [14,] 0.0001073101 0.0001073101 0.0001073101 0.0001073101 0.0000261388
## [15,] 0.0016518190 0.0016518190 0.0016518190 0.0016518190 0.0016518190
## [16,] 0.0121160736 0.0121160736 0.0121160736 0.0121160736 0.0020778759
## [17,] 0.0117042540 0.0004085804 0.0004085804 0.0004085804 0.0117042540
## [18,] 0.0013776507 0.0023213429 0.0023213429 0.0017946119 0.0023213429
## [19,] 0.0162544437 0.0162544437 0.0162544437 0.0682428330 0.0162544437
## [,61] [,62] [,63]
## [1,] 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.0000000000 0.0000000000
## [6,] 0.0000000000 0.0000000000 0.0000000000
## [7,] 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.0000000000 0.0000000000
## [9,] 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0002376186 0.0002358821 0.0002331655
## [12,] 0.0021021822 0.0021021822 0.0018735572
## [13,] 0.0041758292 0.0041758292 0.0035722463
## [14,] 0.0000261388 0.0000261388 0.0000261388
## [15,] 0.0016518190 0.0016518190 0.0016518190
## [16,] 0.0020778759 0.0020778759 0.0020778759
## [17,] 0.0117042540 0.0117042540 0.0004085804
## [18,] 0.0023213429 0.0017946119 0.0031104193
## [19,] 0.0162544437 0.0682428330 0.0682428330
##
## $relative_probs_of_each_state_at_branch_bottom_below_node_DOWNPASS
## [,1] [,2] [,3] [,4] [,5] [,6]
## [1,] 0.004588085 0.083582581 0.004588085 0.004588085 0.004588085 0.004588085
## [2,] 0.004588085 0.083582581 0.004588085 0.004588085 0.004588085 0.004588085
## [3,] 0.005149513 0.005149513 0.080214011 0.005149513 0.005149513 0.005149513
## [4,] 0.005149513 0.080214011 0.005149513 0.005149513 0.005149513 0.005149513
## [5,] 0.002266921 0.002266921 0.002266921 0.097509829 0.002266921 0.002266921
## [6,] 0.002266921 0.002266921 0.002266921 0.097509829 0.002266921 0.002266921
## [7,] 0.019999567 0.015185254 0.015185254 0.015185254 0.015185254 0.015185254
## [8,] 0.012641881 0.012641881 0.012641881 0.012641881 0.035259804 0.012641881
## [9,] 0.007865239 0.007865239 0.007865239 0.007865239 0.007865239 0.007865239
## [10,] 0.007865239 0.007865239 0.007865239 0.007865239 0.007865239 0.063919658
## [11,] NA NA NA NA NA NA
## [12,] 0.016549168 0.017461944 0.015124268 0.016780732 0.015064993 0.015064993
## [13,] 0.014078855 0.021294532 0.014257295 0.019243841 0.014078855 0.014078855
## [14,] 0.014378842 0.024585627 0.014631252 0.014378842 0.014378842 0.014378842
## [15,] 0.002455863 0.096376376 0.002455863 0.002455863 0.002455863 0.002455863
## [16,] 0.004312099 0.044759542 0.044759542 0.004312099 0.004312099 0.004312099
## [17,] 0.014799183 0.014799183 0.014799183 0.022315989 0.014799183 0.014799183
## [18,] 0.015421624 0.015421624 0.015421624 0.015421624 0.016707485 0.016358556
## [19,] 0.011560961 0.011560961 0.011560961 0.011560961 0.011560961 0.026653144
## [,7] [,8] [,9] [,10] [,11] [,12]
## [1,] 0.004588085 0.043979624 0.004630373 0.004630373 0.004630373 0.004630373
## [2,] 0.004588085 0.043979624 0.004630373 0.004630373 0.004630373 0.004630373
## [3,] 0.005149513 0.005189698 0.042581312 0.005189698 0.005189698 0.005189698
## [4,] 0.005149513 0.042581312 0.005189698 0.005189698 0.005189698 0.005189698
## [5,] 0.002266921 0.002317901 0.002317901 0.049760867 0.002317901 0.002317901
## [6,] 0.002266921 0.002317901 0.002317901 0.049760867 0.002317901 0.002317901
## [7,] 0.015185254 0.017585971 0.017585971 0.017585971 0.017585971 0.017585971
## [8,] 0.012641881 0.012653992 0.012653992 0.012653992 0.023920578 0.012653992
## [9,] 0.063919658 0.007895247 0.007895247 0.007895247 0.007895247 0.007895247
## [10,] 0.007865239 0.007895247 0.007895247 0.007895247 0.007895247 0.035817438
## [11,] NA NA NA NA NA NA
## [12,] 0.015064993 0.017001316 0.015836857 0.016661986 0.015807331 0.015807331
## [13,] 0.014078855 0.017679901 0.014174467 0.016658398 0.014085582 0.014085582
## [14,] 0.014378842 0.019468714 0.014510176 0.014384444 0.014384444 0.014384444
## [15,] 0.002455863 0.049290337 0.002506131 0.002506131 0.002506131 0.002506131
## [16,] 0.004312099 0.024504705 0.024504705 0.004355439 0.004355439 0.004355439
## [17,] 0.014799183 0.014803211 0.014803211 0.018547531 0.014803211 0.014803211
## [18,] 0.016358556 0.015423318 0.015423318 0.015423318 0.016063840 0.015890029
## [19,] 0.026653144 0.011577121 0.011577121 0.011577121 0.011577121 0.019094938
## [,13] [,14] [,15] [,16] [,17] [,18]
## [1,] 0.004630373 0.043979624 0.043979624 0.043979624 0.043979624 0.043979624
## [2,] 0.004630373 0.043979624 0.043979624 0.043979624 0.043979624 0.043979624
## [3,] 0.005189698 0.042581312 0.005189698 0.005189698 0.005189698 0.005189698
## [4,] 0.005189698 0.042581312 0.042581312 0.042581312 0.042581312 0.042581312
## [5,] 0.002317901 0.002317901 0.049760867 0.002317901 0.002317901 0.002317901
## [6,] 0.002317901 0.002317901 0.049760867 0.002317901 0.002317901 0.002317901
## [7,] 0.017585971 0.015187834 0.015187834 0.015187834 0.015187834 0.015187834
## [8,] 0.012653992 0.012653992 0.012653992 0.023920578 0.012653992 0.012653992
## [9,] 0.035817438 0.007895247 0.007895247 0.007895247 0.007895247 0.035817438
## [10,] 0.007895247 0.007895247 0.007895247 0.007895247 0.035817438 0.007895247
## [11,] NA NA NA NA NA NA
## [12,] 0.015807331 0.016291535 0.017116664 0.016262009 0.016262009 0.016262009
## [13,] 0.014085582 0.017768787 0.020252717 0.017679901 0.017679901 0.017679901
## [14,] 0.014384444 0.019594446 0.019468714 0.019468714 0.019468714 0.019468714
## [15,] 0.002506131 0.049290337 0.049290337 0.049290337 0.049290337 0.049290337
## [16,] 0.004355439 0.044688303 0.024504705 0.024504705 0.024504705 0.024504705
## [17,] 0.014803211 0.014803211 0.018547531 0.014803211 0.014803211 0.014803211
## [18,] 0.015890029 0.015423318 0.015423318 0.016063840 0.015890029 0.015890029
## [19,] 0.019094938 0.011577121 0.011577121 0.011577121 0.019094938 0.019094938
## [,19] [,20] [,21] [,22] [,23] [,24]
## [1,] 0.004630373 0.004630373 0.004630373 0.004630373 0.004630373 0.004630373
## [2,] 0.004630373 0.004630373 0.004630373 0.004630373 0.004630373 0.004630373
## [3,] 0.042581312 0.042581312 0.042581312 0.042581312 0.005189698 0.005189698
## [4,] 0.005189698 0.005189698 0.005189698 0.005189698 0.005189698 0.005189698
## [5,] 0.049760867 0.002317901 0.002317901 0.002317901 0.049760867 0.049760867
## [6,] 0.049760867 0.002317901 0.002317901 0.002317901 0.049760867 0.049760867
## [7,] 0.015187834 0.015187834 0.015187834 0.015187834 0.015187834 0.015187834
## [8,] 0.012653992 0.023920578 0.012653992 0.012653992 0.023920578 0.012653992
## [9,] 0.007895247 0.007895247 0.007895247 0.035817438 0.007895247 0.007895247
## [10,] 0.007895247 0.007895247 0.035817438 0.007895247 0.007895247 0.035817438
## [11,] NA NA NA NA NA NA
## [12,] 0.015952205 0.015097551 0.015097551 0.015097551 0.015922679 0.015922679
## [13,] 0.016747283 0.014174467 0.014174467 0.014174467 0.016658398 0.016658398
## [14,] 0.014510176 0.014510176 0.014510176 0.014510176 0.014384444 0.014384444
## [15,] 0.002506131 0.002506131 0.002506131 0.002506131 0.002506131 0.002506131
## [16,] 0.024504705 0.024504705 0.024504705 0.024504705 0.004355439 0.004355439
## [17,] 0.018547531 0.014803211 0.014803211 0.014803211 0.018547531 0.018547531
## [18,] 0.015423318 0.016063840 0.015890029 0.015890029 0.016063840 0.015890029
## [19,] 0.011577121 0.011577121 0.019094938 0.019094938 0.011577121 0.019094938
## [,25] [,26] [,27] [,28] [,29] [,30]
## [1,] 0.004630373 0.004630373 0.004630373 0.004630373 0.030982470 0.030982470
## [2,] 0.004630373 0.004630373 0.004630373 0.004630373 0.030982470 0.030982470
## [3,] 0.005189698 0.005189698 0.005189698 0.005189698 0.030230770 0.005104701
## [4,] 0.005189698 0.005189698 0.005189698 0.005189698 0.030230770 0.030230770
## [5,] 0.049760867 0.002317901 0.002317901 0.002317901 0.002210047 0.034090267
## [6,] 0.049760867 0.002317901 0.002317901 0.002317901 0.002210047 0.034090267
## [7,] 0.015187834 0.015187834 0.015187834 0.015187834 0.016793861 0.016793861
## [8,] 0.012653992 0.023920578 0.023920578 0.012653992 0.012628381 0.012628381
## [9,] 0.035817438 0.007895247 0.035817438 0.035817438 0.007831776 0.007831776
## [10,] 0.007895247 0.035817438 0.007895247 0.035817438 0.007831776 0.007831776
## [11,] NA NA NA NA NA NA
## [12,] 0.015922679 0.015068024 0.015068024 0.015068024 0.016380576 0.016935038
## [13,] 0.016658398 0.014085582 0.014085582 0.014085582 0.016546367 0.018215495
## [14,] 0.014384444 0.014384444 0.014384444 0.014384444 0.017873570 0.017789082
## [15,] 0.002506131 0.002506131 0.002506131 0.002506131 0.033837272 0.033837272
## [16,] 0.004355439 0.004355439 0.004355439 0.004355439 0.031380257 0.017804552
## [17,] 0.018547531 0.014803211 0.014803211 0.014803211 0.014794699 0.017310773
## [18,] 0.015890029 0.016530551 0.016530551 0.016356740 0.015419740 0.015419740
## [19,] 0.019094938 0.019094938 0.019094938 0.026612754 0.011542943 0.011542943
## [,31] [,32] [,33] [,34] [,35] [,36]
## [1,] 0.030982470 0.030982470 0.030982470 0.004540926 0.004540926 0.004540926
## [2,] 0.030982470 0.030982470 0.030982470 0.004540926 0.004540926 0.004540926
## [3,] 0.005104701 0.005104701 0.005104701 0.030230770 0.030230770 0.030230770
## [4,] 0.030230770 0.030230770 0.030230770 0.005104701 0.005104701 0.005104701
## [5,] 0.002210047 0.002210047 0.002210047 0.034090267 0.002210047 0.002210047
## [6,] 0.002210047 0.002210047 0.002210047 0.034090267 0.002210047 0.002210047
## [7,] 0.016793861 0.016793861 0.016793861 0.016793861 0.016793861 0.016793861
## [8,] 0.020199197 0.012628381 0.012628381 0.012628381 0.020199197 0.012628381
## [9,] 0.007831776 0.007831776 0.026594670 0.007831776 0.007831776 0.007831776
## [10,] 0.007831776 0.026594670 0.007831776 0.007831776 0.007831776 0.026594670
## [11,] NA NA NA NA NA NA
## [12,] 0.016360735 0.016360735 0.016360735 0.016152556 0.015578253 0.015578253
## [13,] 0.016486638 0.016486638 0.016486638 0.015859946 0.014131089 0.014131089
## [14,] 0.017789082 0.017789082 0.017789082 0.014457089 0.014457089 0.014457089
## [15,] 0.033837272 0.033837272 0.033837272 0.002399769 0.002399769 0.002399769
## [16,] 0.017804552 0.017804552 0.017804552 0.017804552 0.017804552 0.017804552
## [17,] 0.014794699 0.014794699 0.014794699 0.017310773 0.014794699 0.014794699
## [18,] 0.015850152 0.015733356 0.015733356 0.015419740 0.015850152 0.015733356
## [19,] 0.011542943 0.016594695 0.016594695 0.011542943 0.011542943 0.016594695
## [,37] [,38] [,39] [,40] [,41] [,42]
## [1,] 0.004540926 0.004540926 0.004540926 0.004540926 0.004540926 0.004540926
## [2,] 0.004540926 0.004540926 0.004540926 0.004540926 0.004540926 0.004540926
## [3,] 0.030230770 0.005104701 0.005104701 0.005104701 0.005104701 0.005104701
## [4,] 0.005104701 0.005104701 0.005104701 0.005104701 0.005104701 0.005104701
## [5,] 0.002210047 0.034090267 0.034090267 0.034090267 0.002210047 0.002210047
## [6,] 0.002210047 0.034090267 0.034090267 0.034090267 0.002210047 0.002210047
## [7,] 0.016793861 0.016793861 0.016793861 0.016793861 0.016793861 0.016793861
## [8,] 0.012628381 0.020199197 0.012628381 0.012628381 0.020199197 0.020199197
## [9,] 0.026594670 0.007831776 0.007831776 0.026594670 0.007831776 0.026594670
## [10,] 0.007831776 0.007831776 0.026594670 0.007831776 0.026594670 0.007831776
## [11,] NA NA NA NA NA NA
## [12,] 0.015578253 0.016132715 0.016132715 0.016132715 0.015558412 0.015558412
## [13,] 0.014131089 0.015800218 0.015800218 0.015800218 0.014071361 0.014071361
## [14,] 0.014457089 0.014372601 0.014372601 0.014372601 0.014372601 0.014372601
## [15,] 0.002399769 0.002399769 0.002399769 0.002399769 0.002399769 0.002399769
## [16,] 0.017804552 0.004263836 0.004263836 0.004263836 0.004263836 0.004263836
## [17,] 0.014794699 0.017310773 0.017310773 0.017310773 0.014794699 0.014794699
## [18,] 0.015733356 0.015850152 0.015733356 0.015733356 0.016163768 0.016163768
## [19,] 0.016594695 0.011542943 0.016594695 0.016594695 0.016594695 0.016594695
## [,43] [,44] [,45] [,46] [,47] [,48]
## [1,] 0.004540926 0.030982470 0.030982470 0.030982470 0.030982470 0.030982470
## [2,] 0.004540926 0.030982470 0.030982470 0.030982470 0.030982470 0.030982470
## [3,] 0.005104701 0.030230770 0.030230770 0.030230770 0.030230770 0.005104701
## [4,] 0.005104701 0.030230770 0.030230770 0.030230770 0.030230770 0.030230770
## [5,] 0.002210047 0.034090267 0.002210047 0.002210047 0.002210047 0.034090267
## [6,] 0.002210047 0.034090267 0.002210047 0.002210047 0.002210047 0.034090267
## [7,] 0.016793861 0.015182383 0.015182383 0.015182383 0.015182383 0.015182383
## [8,] 0.012628381 0.012628381 0.020199197 0.012628381 0.012628381 0.020199197
## [9,] 0.026594670 0.007831776 0.007831776 0.007831776 0.026594670 0.007831776
## [10,] 0.026594670 0.007831776 0.007831776 0.026594670 0.007831776 0.007831776
## [11,] NA NA NA NA NA NA
## [12,] 0.015558412 0.016458086 0.015883783 0.015883783 0.015883783 0.016438245
## [13,] 0.014071361 0.018275224 0.016546367 0.016546367 0.016546367 0.018215495
## [14,] 0.014372601 0.017873570 0.017873570 0.017873570 0.017873570 0.017789082
## [15,] 0.002399769 0.033837272 0.033837272 0.033837272 0.033837272 0.033837272
## [16,] 0.004263836 0.031380257 0.031380257 0.031380257 0.031380257 0.017804552
## [17,] 0.014794699 0.017310773 0.014794699 0.014794699 0.014794699 0.017310773
## [18,] 0.016046972 0.015419740 0.015850152 0.015733356 0.015733356 0.015850152
## [19,] 0.021646447 0.011542943 0.011542943 0.016594695 0.016594695 0.011542943
## [,49] [,50] [,51] [,52] [,53] [,54]
## [1,] 0.030982470 0.030982470 0.030982470 0.030982470 0.030982470 0.004540926
## [2,] 0.030982470 0.030982470 0.030982470 0.030982470 0.030982470 0.004540926
## [3,] 0.005104701 0.005104701 0.005104701 0.005104701 0.005104701 0.030230770
## [4,] 0.030230770 0.030230770 0.030230770 0.030230770 0.030230770 0.005104701
## [5,] 0.034090267 0.034090267 0.002210047 0.002210047 0.002210047 0.034090267
## [6,] 0.034090267 0.034090267 0.002210047 0.002210047 0.002210047 0.034090267
## [7,] 0.015182383 0.015182383 0.015182383 0.015182383 0.015182383 0.015182383
## [8,] 0.012628381 0.012628381 0.020199197 0.020199197 0.012628381 0.020199197
## [9,] 0.007831776 0.026594670 0.007831776 0.026594670 0.026594670 0.007831776
## [10,] 0.026594670 0.007831776 0.026594670 0.007831776 0.026594670 0.007831776
## [11,] NA NA NA NA NA NA
## [12,] 0.016438245 0.016438245 0.015863942 0.015863942 0.015863942 0.015655763
## [13,] 0.018215495 0.018215495 0.016486638 0.016486638 0.016486638 0.015859946
## [14,] 0.017789082 0.017789082 0.017789082 0.017789082 0.017789082 0.014457089
## [15,] 0.033837272 0.033837272 0.033837272 0.033837272 0.033837272 0.002399769
## [16,] 0.017804552 0.017804552 0.017804552 0.017804552 0.017804552 0.017804552
## [17,] 0.017310773 0.017310773 0.014794699 0.014794699 0.014794699 0.017310773
## [18,] 0.015733356 0.015733356 0.016163768 0.016163768 0.016046972 0.015850152
## [19,] 0.016594695 0.016594695 0.016594695 0.016594695 0.021646447 0.011542943
## [,55] [,56] [,57] [,58] [,59] [,60]
## [1,] 0.004540926 0.004540926 0.004540926 0.004540926 0.004540926 0.004540926
## [2,] 0.004540926 0.004540926 0.004540926 0.004540926 0.004540926 0.004540926
## [3,] 0.030230770 0.030230770 0.030230770 0.030230770 0.030230770 0.005104701
## [4,] 0.005104701 0.005104701 0.005104701 0.005104701 0.005104701 0.005104701
## [5,] 0.034090267 0.034090267 0.002210047 0.002210047 0.002210047 0.034090267
## [6,] 0.034090267 0.034090267 0.002210047 0.002210047 0.002210047 0.034090267
## [7,] 0.015182383 0.015182383 0.015182383 0.015182383 0.015182383 0.015182383
## [8,] 0.012628381 0.012628381 0.020199197 0.020199197 0.012628381 0.020199197
## [9,] 0.007831776 0.026594670 0.007831776 0.026594670 0.026594670 0.007831776
## [10,] 0.026594670 0.007831776 0.026594670 0.007831776 0.026594670 0.026594670
## [11,] NA NA NA NA NA NA
## [12,] 0.015655763 0.015655763 0.015081460 0.015081460 0.015081460 0.015635922
## [13,] 0.015859946 0.015859946 0.014131089 0.014131089 0.014131089 0.015800218
## [14,] 0.014457089 0.014457089 0.014457089 0.014457089 0.014457089 0.014372601
## [15,] 0.002399769 0.002399769 0.002399769 0.002399769 0.002399769 0.002399769
## [16,] 0.017804552 0.017804552 0.017804552 0.017804552 0.017804552 0.004263836
## [17,] 0.017310773 0.017310773 0.014794699 0.014794699 0.014794699 0.017310773
## [18,] 0.015733356 0.015733356 0.016163768 0.016163768 0.016046972 0.016163768
## [19,] 0.016594695 0.016594695 0.016594695 0.016594695 0.021646447 0.016594695
## [,61] [,62] [,63]
## [1,] 0.004540926 0.004540926 0.004540926
## [2,] 0.004540926 0.004540926 0.004540926
## [3,] 0.005104701 0.005104701 0.005104701
## [4,] 0.005104701 0.005104701 0.005104701
## [5,] 0.034090267 0.034090267 0.002210047
## [6,] 0.034090267 0.034090267 0.002210047
## [7,] 0.015182383 0.015182383 0.015182383
## [8,] 0.020199197 0.012628381 0.020199197
## [9,] 0.026594670 0.026594670 0.026594670
## [10,] 0.007831776 0.026594670 0.026594670
## [11,] NA NA NA
## [12,] 0.015635922 0.015635922 0.015061619
## [13,] 0.015800218 0.015800218 0.014071361
## [14,] 0.014372601 0.014372601 0.014372601
## [15,] 0.002399769 0.002399769 0.002399769
## [16,] 0.004263836 0.004263836 0.004263836
## [17,] 0.017310773 0.017310773 0.014794699
## [18,] 0.016163768 0.016046972 0.016477384
## [19,] 0.016594695 0.021646447 0.021646447
##
## $relative_probs_of_each_state_at_branch_bottom_below_node_UPPASS
## [,1] [,2] [,3] [,4] [,5] [,6]
## [1,] 0.009570786 0.89930933 0.052884137 0.009683003 0.009472930 0.009473018
## [2,] 0.009570786 0.89930933 0.052884137 0.009683003 0.009472930 0.009473018
## [3,] 0.004642347 0.97215236 0.004607358 0.004682604 0.004607242 0.004607273
## [4,] 0.025403955 0.51873793 0.354366287 0.025726943 0.025122299 0.025122552
## [5,] 0.023552518 0.02415295 0.023275220 0.859038152 0.023251969 0.023252239
## [6,] 0.023552518 0.02415295 0.023275220 0.859038152 0.023251969 0.023252239
## [7,] 0.127102054 0.19052085 0.128670369 0.172497262 0.126971739 0.127007101
## [8,] 0.104922872 0.10490666 0.104948186 0.104918758 0.104949239 0.237565382
## [9,] 0.069460811 0.06945708 0.069466640 0.069459864 0.111370751 0.541087144
## [10,] 0.069460811 0.06945708 0.069466640 0.069459864 0.111370751 0.069466882
## [11,] NA NA NA NA NA NA
## [12,] 0.103135147 0.10313515 0.103135147 0.103135147 0.103244146 0.103214569
## [13,] 0.179143825 0.13682962 0.136829618 0.136829618 0.136689194 0.136727299
## [14,] 0.159240541 0.12945162 0.129451623 0.193520382 0.129352757 0.129379585
## [15,] 0.041955876 0.39573770 0.395737703 0.042872210 0.041156805 0.041157523
## [16,] 0.025373402 0.84887322 0.024905012 0.025912311 0.024903457 0.024903879
## [17,] 0.154950929 0.21304264 0.128126295 0.125973103 0.125876929 0.125903027
## [18,] 0.103230726 0.10330810 0.103109941 0.103250355 0.103104917 0.103104917
## [19,] 0.114419631 0.11440192 0.114447273 0.114415139 0.313195661 0.114448423
## [,7] [,8] [,9] [,10] [,11]
## [1,] 0.009473018 1.848848e-06 1.113819e-05 6.635310e-06 6.613414e-06
## [2,] 0.009473018 1.848848e-06 1.113819e-05 6.635310e-06 6.613414e-06
## [3,] 0.004607273 1.730383e-06 5.544256e-06 5.551151e-06 5.544246e-06
## [4,] 0.025122552 5.434389e-05 4.137526e-06 9.173419e-06 9.118019e-06
## [5,] 0.023252239 1.454186e-05 1.435121e-05 1.529913e-06 1.434616e-05
## [6,] 0.023252239 1.454186e-05 1.435121e-05 1.529913e-06 1.434616e-05
## [7,] 0.127007101 1.015944e-05 1.110353e-05 1.043455e-05 1.112425e-05
## [8,] 0.237565382 1.179923e-05 1.180061e-05 1.179963e-05 1.180065e-05
## [9,] 0.069466882 1.245280e-05 1.245333e-05 1.245296e-05 1.478272e-05
## [10,] 0.541087144 1.245280e-05 1.245333e-05 1.245296e-05 1.478272e-05
## [11,] NA NA NA NA NA
## [12,] 0.103214569 1.337820e-02 1.337820e-02 1.337820e-02 1.316388e-02
## [13,] 0.136727299 1.018486e-05 1.018486e-05 1.018486e-05 1.018202e-05
## [14,] 0.129379585 1.143121e-05 1.143121e-05 1.037699e-05 1.142896e-05
## [15,] 0.041157523 8.361805e-06 8.361805e-06 1.400153e-05 1.381022e-05
## [16,] 0.024903879 1.660493e-06 1.432219e-05 1.452425e-05 1.432188e-05
## [17,] 0.125903027 1.012615e-05 1.152341e-05 1.155884e-05 1.155655e-05
## [18,] 0.103104917 1.285021e-02 1.323983e-02 1.296375e-02 1.324971e-02
## [19,] 0.114448423 1.150942e-05 1.151075e-05 1.150981e-05 8.477346e-06
## [,12] [,13] [,14] [,15] [,16]
## [1,] 6.613423e-06 6.613423e-06 2.700661e-06 1.851055e-06 1.846924e-06
## [2,] 6.613423e-06 6.613423e-06 2.700661e-06 1.851055e-06 1.846924e-06
## [3,] 5.544249e-06 5.544249e-06 1.729692e-06 1.731178e-06 1.729690e-06
## [4,] 9.118042e-06 9.118042e-06 1.387759e-05 5.437348e-05 5.431808e-05
## [5,] 1.434622e-05 1.434622e-05 1.448163e-05 1.541263e-06 1.447658e-05
## [6,] 1.434622e-05 1.434622e-05 1.448163e-05 1.541263e-06 1.447658e-05
## [7,] 1.112512e-05 1.112512e-05 1.013550e-05 9.466519e-06 1.015655e-05
## [8,] 9.776554e-06 9.776554e-06 1.180007e-05 1.179909e-05 1.180011e-05
## [9,] 5.257340e-06 1.245335e-05 1.245313e-05 1.245275e-05 1.478251e-05
## [10,] 1.245335e-05 5.257340e-06 1.245313e-05 1.245275e-05 1.478251e-05
## [11,] NA NA NA NA NA
## [12,] 1.322204e-02 1.322204e-02 1.337820e-02 1.337820e-02 1.316388e-02
## [13,] 1.018279e-05 1.018279e-05 1.083075e-05 1.083075e-05 1.082769e-05
## [14,] 1.142957e-05 1.142957e-05 1.075255e-05 9.774733e-06 1.075030e-05
## [15,] 1.381030e-05 1.381030e-05 2.897473e-06 8.421890e-06 8.309408e-06
## [16,] 1.432196e-05 1.432196e-05 1.651586e-06 1.670740e-06 1.651557e-06
## [17,] 1.155717e-05 1.155717e-05 9.505080e-06 9.537942e-06 9.535990e-06
## [18,] 1.324971e-02 1.324971e-02 1.308770e-02 1.281162e-02 1.309758e-02
## [19,] 1.151078e-05 1.151078e-05 1.151023e-05 1.150929e-05 8.476989e-06
## [,17] [,18] [,19] [,20] [,21]
## [1,] 1.846926e-06 1.846926e-06 1.114988e-05 1.112799e-05 1.112800e-05
## [2,] 1.846926e-06 1.846926e-06 1.114988e-05 1.112799e-05 1.112800e-05
## [3,] 1.729691e-06 1.729691e-06 5.547945e-06 5.541040e-06 5.541043e-06
## [4,] 5.431810e-05 5.431810e-05 4.143903e-06 4.131965e-06 4.131970e-06
## [5,] 1.447664e-05 1.447664e-05 1.524672e-06 1.428594e-05 1.428599e-05
## [6,] 1.447664e-05 1.447664e-05 1.524672e-06 1.428594e-05 1.428599e-05
## [7,] 1.015734e-05 1.015734e-05 1.041061e-05 1.110032e-05 1.110119e-05
## [8,] 9.776120e-06 9.776120e-06 1.180047e-05 1.180149e-05 9.777230e-06
## [9,] 5.257266e-06 1.245314e-05 1.245328e-05 1.478304e-05 5.257457e-06
## [10,] 1.245314e-05 5.257266e-06 1.245328e-05 1.478304e-05 1.245367e-05
## [11,] NA NA NA NA NA
## [12,] 1.322204e-02 1.322204e-02 1.337820e-02 1.316388e-02 1.322204e-02
## [13,] 1.082852e-05 1.082852e-05 1.083075e-05 1.082769e-05 1.082852e-05
## [14,] 1.075091e-05 1.075091e-05 9.774733e-06 1.075030e-05 1.075091e-05
## [15,] 8.309455e-06 8.309455e-06 8.421890e-06 8.309408e-06 8.309455e-06
## [16,] 1.651565e-06 1.651565e-06 1.443029e-05 1.422792e-05 1.422800e-05
## [17,] 9.536520e-06 9.536520e-06 1.083394e-05 1.083165e-05 1.083227e-05
## [18,] 1.309758e-02 1.309758e-02 1.320124e-02 1.348720e-02 1.348720e-02
## [19,] 1.151027e-05 1.151027e-05 1.151062e-05 8.477904e-06 1.151159e-05
## [,22] [,23] [,24] [,25] [,26]
## [1,] 1.112800e-05 6.625110e-06 6.625119e-06 6.625119e-06 6.603223e-06
## [2,] 1.112800e-05 6.625110e-06 6.625119e-06 6.625119e-06 6.603223e-06
## [3,] 5.541043e-06 5.547934e-06 5.547937e-06 5.547937e-06 5.541032e-06
## [4,] 4.131970e-06 9.147613e-06 9.147636e-06 9.147636e-06 9.092236e-06
## [5,] 1.428599e-05 1.524232e-06 1.524237e-06 1.524237e-06 1.428094e-05
## [6,] 1.428599e-05 1.524232e-06 1.524237e-06 1.524237e-06 1.428094e-05
## [7,] 1.110119e-05 1.043157e-05 1.043238e-05 1.043238e-05 1.112190e-05
## [8,] 9.777230e-06 1.180051e-05 9.776444e-06 9.776444e-06 9.777258e-06
## [9,] 1.245367e-05 1.478267e-05 5.257321e-06 1.245330e-05 6.095348e-06
## [10,] 5.257457e-06 1.478267e-05 1.245330e-05 5.257321e-06 1.478306e-05
## [11,] NA NA NA NA NA
## [12,] 1.322204e-02 1.316388e-02 1.322204e-02 1.322204e-02 1.300773e-02
## [13,] 1.082852e-05 1.082769e-05 1.082852e-05 1.082852e-05 1.082545e-05
## [14,] 1.075091e-05 9.772734e-06 9.773276e-06 9.773276e-06 1.074866e-05
## [15,] 8.309455e-06 1.391241e-05 1.391249e-05 1.391249e-05 1.372118e-05
## [16,] 1.422800e-05 1.442998e-05 1.443006e-05 1.443006e-05 1.422769e-05
## [17,] 1.083227e-05 1.086450e-05 1.086512e-05 1.086512e-05 1.086283e-05
## [18,] 1.348720e-02 1.321112e-02 1.321112e-02 1.321112e-02 1.349708e-02
## [19,] 1.151159e-05 8.477256e-06 1.151065e-05 1.151065e-05 8.477927e-06
## [,27] [,28] [,29] [,30] [,31]
## [1,] 6.603223e-06 6.603232e-06 2.263239e-11 1.374504e-11 1.370182e-11
## [2,] 6.603223e-06 6.603232e-06 2.263239e-11 1.374504e-11 1.370182e-11
## [3,] 5.541032e-06 5.541035e-06 1.440101e-11 1.441645e-11 1.440099e-11
## [4,] 9.092236e-06 9.092259e-06 1.155415e-10 5.153991e-10 5.148461e-10
## [5,] 1.428094e-05 1.428100e-05 1.421474e-10 1.373379e-11 1.420971e-10
## [6,] 1.428094e-05 1.428100e-05 1.421474e-10 1.373379e-11 1.420971e-10
## [7,] 1.112190e-05 1.112278e-05 8.296372e-11 7.635534e-11 8.317125e-11
## [8,] 9.777258e-06 7.752993e-06 1.027269e-10 1.027171e-10 1.027272e-10
## [9,] 1.478306e-05 5.257462e-06 1.123986e-10 1.123948e-10 1.356713e-10
## [10,] 6.095348e-06 5.257462e-06 1.123986e-10 1.123948e-10 1.356713e-10
## [11,] NA NA NA NA NA
## [12,] 1.300773e-02 1.306588e-02 1.088472e-07 1.088472e-07 1.067256e-07
## [13,] 1.082545e-05 1.082628e-05 8.198590e-11 8.198590e-11 8.195739e-11
## [14,] 1.074866e-05 1.074927e-05 9.397402e-11 8.356088e-11 9.395144e-11
## [15,] 1.372118e-05 1.372126e-05 2.444560e-11 7.939867e-11 7.826749e-11
## [16,] 1.422769e-05 1.422778e-05 1.457666e-11 1.478701e-11 1.457634e-11
## [17,] 1.086283e-05 1.086345e-05 8.129983e-11 8.164979e-11 8.163017e-11
## [18,] 1.349708e-02 1.349708e-02 1.041109e-07 1.013778e-07 1.042087e-07
## [19,] 8.477927e-06 1.151162e-05 9.843230e-11 9.842291e-11 6.847155e-11
## [,32] [,33] [,34] [,35] [,36]
## [1,] 1.370184e-11 1.370184e-11 6.949858e-11 6.928007e-11 6.928016e-11
## [2,] 1.370184e-11 1.370184e-11 6.949858e-11 6.928007e-11 6.928016e-11
## [3,] 1.440099e-11 1.440099e-11 7.974964e-12 7.906043e-12 7.906072e-12
## [4,] 5.148463e-10 5.148463e-10 1.435932e-11 1.423523e-11 1.423528e-11
## [5,] 1.420977e-10 1.420977e-10 1.355004e-11 1.401958e-10 1.401964e-10
## [6,] 1.420977e-10 1.420977e-10 1.355004e-11 1.401958e-10 1.401964e-10
## [7,] 8.317911e-11 8.317911e-11 8.568138e-11 9.249404e-11 9.250278e-11
## [8,] 8.273540e-11 8.273540e-11 1.027309e-10 1.027411e-10 8.274654e-11
## [9,] 4.131784e-11 1.123987e-10 1.124001e-10 1.356766e-10 4.131980e-11
## [10,] 1.123987e-10 4.131784e-11 1.124001e-10 1.356766e-10 1.124040e-10
## [11,] NA NA NA NA NA
## [12,] 1.073013e-07 1.073013e-07 1.088472e-07 1.067256e-07 1.073013e-07
## [13,] 8.196513e-11 8.196513e-11 8.198590e-11 8.195739e-11 8.196513e-11
## [14,] 9.395756e-11 9.395756e-11 8.356088e-11 9.395144e-11 9.395756e-11
## [15,] 7.826796e-11 7.826796e-11 7.939867e-11 7.826749e-11 7.826796e-11
## [16,] 1.457643e-11 1.457643e-11 1.416671e-10 1.396488e-10 1.396496e-10
## [17,] 8.163549e-11 8.163549e-11 9.545130e-11 9.542837e-11 9.543459e-11
## [18,] 1.042087e-07 1.042087e-07 1.052349e-07 1.080658e-07 1.080658e-07
## [19,] 9.843264e-11 9.843264e-11 9.843617e-11 6.848077e-11 9.844590e-11
## [,37] [,38] [,39] [,40] [,41]
## [1,] 6.928016e-11 2.434320e-11 2.434329e-11 2.434329e-11 2.412478e-11
## [2,] 6.928016e-11 2.434320e-11 2.434329e-11 2.434329e-11 2.412478e-11
## [3,] 7.906072e-12 7.974858e-12 7.974887e-12 7.974887e-12 7.905966e-12
## [4,] 1.423528e-11 6.398352e-11 6.398376e-11 6.398376e-11 6.343079e-11
## [5,] 1.401964e-10 1.354517e-11 1.354523e-11 1.354523e-11 1.401460e-10
## [6,] 1.401964e-10 1.354517e-11 1.354523e-11 1.354523e-11 1.401460e-10
## [7,] 9.250278e-11 8.588797e-11 8.589608e-11 8.589608e-11 9.270693e-11
## [8,] 8.274654e-11 1.027313e-10 8.273864e-11 8.273864e-11 8.274682e-11
## [9,] 1.124040e-10 1.356728e-10 4.131841e-11 1.124002e-10 4.987486e-11
## [10,] 4.131980e-11 1.356728e-10 1.124002e-10 4.131841e-11 1.356767e-10
## [11,] NA NA NA NA NA
## [12,] 1.073013e-07 1.067256e-07 1.073013e-07 1.073013e-07 1.051796e-07
## [13,] 8.196513e-11 8.195739e-11 8.196513e-11 8.196513e-11 8.193661e-11
## [14,] 9.395756e-11 8.354080e-11 8.354625e-11 8.354625e-11 9.393498e-11
## [15,] 7.826796e-11 1.339960e-10 1.339968e-10 1.339968e-10 1.320878e-10
## [16,] 1.396496e-10 1.416640e-10 1.416648e-10 1.416648e-10 1.396465e-10
## [17,] 9.543459e-11 9.577824e-11 9.578449e-11 9.578449e-11 9.576147e-11
## [18,] 1.080658e-07 1.053327e-07 1.053327e-07 1.053327e-07 1.081636e-07
## [19,] 9.844590e-11 6.847424e-11 9.843650e-11 9.843650e-11 6.848101e-11
## [,42] [,43] [,44] [,45] [,46]
## [1,] 2.412478e-11 2.412487e-11 2.265548e-11 2.261226e-11 2.261228e-11
## [2,] 2.412478e-11 2.412487e-11 2.265548e-11 2.261226e-11 2.261228e-11
## [3,] 7.905966e-12 7.905994e-12 1.440927e-11 1.439381e-11 1.439381e-11
## [4,] 6.343079e-11 6.343102e-11 1.156078e-10 1.154837e-10 1.154838e-10
## [5,] 1.401460e-10 1.401466e-10 1.367574e-11 1.414964e-10 1.414970e-10
## [6,] 1.401460e-10 1.401466e-10 1.367574e-11 1.414964e-10 1.414970e-10
## [7,] 9.270693e-11 9.271568e-11 7.611887e-11 8.293486e-11 8.294269e-11
## [8,] 8.274682e-11 6.275222e-11 1.027255e-10 1.027357e-10 8.274219e-11
## [9,] 1.356767e-10 4.131985e-11 1.123980e-10 1.356745e-10 4.131903e-11
## [10,] 4.987486e-11 4.131985e-11 1.123980e-10 1.356745e-10 1.124019e-10
## [11,] NA NA NA NA NA
## [12,] 1.051796e-07 1.057554e-07 1.088472e-07 1.067256e-07 1.073013e-07
## [13,] 8.193661e-11 8.194435e-11 8.836619e-11 8.833545e-11 8.834380e-11
## [14,] 9.393498e-11 9.394111e-11 7.751064e-11 8.714724e-11 8.715337e-11
## [15,] 1.320878e-10 1.320886e-10 2.463433e-11 2.428103e-11 2.428118e-11
## [16,] 1.396465e-10 1.396474e-10 1.468920e-11 1.447853e-11 1.447862e-11
## [17,] 9.576147e-11 9.576772e-11 7.541331e-11 7.539377e-11 7.539907e-11
## [18,] 1.081636e-07 1.081636e-07 1.037288e-07 1.065598e-07 1.065598e-07
## [19,] 6.848101e-11 9.844623e-11 9.843099e-11 6.847717e-11 9.844072e-11
## [,47] [,48] [,49] [,50] [,51]
## [1,] 2.261228e-11 1.372490e-11 1.372492e-11 1.372492e-11 1.368171e-11
## [2,] 2.261228e-11 1.372490e-11 1.372492e-11 1.372492e-11 1.368171e-11
## [3,] 1.439381e-11 1.440925e-11 1.440926e-11 1.440926e-11 1.439379e-11
## [4,] 1.154838e-10 5.151415e-10 5.151417e-10 5.151417e-10 5.145888e-10
## [5,] 1.414970e-10 1.367087e-11 1.367093e-11 1.367093e-11 1.414466e-10
## [6,] 1.414970e-10 1.367087e-11 1.367093e-11 1.367093e-11 1.414466e-10
## [7,] 8.294269e-11 7.632878e-11 7.633599e-11 7.633599e-11 8.315017e-11
## [8,] 8.274219e-11 1.027259e-10 8.273429e-11 8.273429e-11 8.274247e-11
## [9,] 1.124019e-10 1.356707e-10 4.131765e-11 1.123982e-10 4.987410e-11
## [10,] 4.131903e-11 1.356707e-10 1.123982e-10 4.131765e-11 1.356746e-10
## [11,] NA NA NA NA NA
## [12,] 1.073013e-07 1.067256e-07 1.073013e-07 1.073013e-07 1.051796e-07
## [13,] 8.834380e-11 8.833545e-11 8.834380e-11 8.834380e-11 8.831306e-11
## [14,] 8.715337e-11 7.749056e-11 7.749601e-11 7.749601e-11 8.713078e-11
## [15,] 2.428118e-11 7.887175e-11 7.887222e-11 7.887222e-11 7.774104e-11
## [16,] 1.447862e-11 1.468887e-11 1.468896e-11 1.468896e-11 1.447829e-11
## [17,] 7.539907e-11 7.571831e-11 7.572363e-11 7.572363e-11 7.570401e-11
## [18,] 1.065598e-07 1.038266e-07 1.038266e-07 1.038266e-07 1.066576e-07
## [19,] 9.844072e-11 6.847064e-11 9.843133e-11 9.843133e-11 6.847741e-11
## [,52] [,53] [,54] [,55] [,56]
## [1,] 1.368171e-11 1.368172e-11 6.939680e-11 6.939689e-11 6.939689e-11
## [2,] 1.368171e-11 1.368172e-11 6.939680e-11 6.939689e-11 6.939689e-11
## [3,] 1.439379e-11 1.439379e-11 7.942859e-12 7.942888e-12 7.942888e-12
## [4,] 5.145888e-10 5.145890e-10 1.430152e-11 1.430157e-11 1.430157e-11
## [5,] 1.414466e-10 1.414472e-10 1.348712e-11 1.348718e-11 1.348718e-11
## [6,] 1.414466e-10 1.414472e-10 1.348712e-11 1.348718e-11 1.348718e-11
## [7,] 8.315017e-11 8.315802e-11 8.565158e-11 8.565966e-11 8.565966e-11
## [8,] 8.274247e-11 6.274892e-11 1.027397e-10 8.274543e-11 8.274543e-11
## [9,] 1.356746e-10 4.131908e-11 1.356760e-10 4.131960e-11 1.124035e-10
## [10,] 4.987410e-11 4.131908e-11 1.356760e-10 1.124035e-10 4.131960e-11
## [11,] NA NA NA NA NA
## [12,] 1.051796e-07 1.057554e-07 1.067256e-07 1.073013e-07 1.073013e-07
## [13,] 8.831306e-11 8.832140e-11 8.833545e-11 8.834380e-11 8.834380e-11
## [14,] 8.713078e-11 8.713691e-11 7.749056e-11 7.749601e-11 7.749601e-11
## [15,] 7.774104e-11 7.774151e-11 7.887175e-11 7.887222e-11 7.887222e-11
## [16,] 1.447829e-11 1.447838e-11 1.407269e-10 1.407278e-10 1.407278e-10
## [17,] 7.570401e-11 7.570934e-11 8.851721e-11 8.852343e-11 8.852343e-11
## [18,] 1.066576e-07 1.066576e-07 1.076838e-07 1.076838e-07 1.076838e-07
## [19,] 6.847741e-11 9.844106e-11 6.847986e-11 9.844458e-11 9.844458e-11
## [,57] [,58] [,59] [,60] [,61]
## [1,] 6.917837e-11 6.917837e-11 6.917846e-11 2.424150e-11 2.424150e-11
## [2,] 6.917837e-11 6.917837e-11 6.917846e-11 2.424150e-11 2.424150e-11
## [3,] 7.873967e-12 7.873967e-12 7.873996e-12 7.942782e-12 7.942782e-12
## [4,] 1.417747e-11 1.417747e-11 1.417752e-11 6.372617e-11 6.372617e-11
## [5,] 1.395454e-10 1.395454e-10 1.395460e-10 1.348231e-11 1.348231e-11
## [6,] 1.395454e-10 1.395454e-10 1.395460e-10 1.348231e-11 1.348231e-11
## [7,] 9.247060e-11 9.247060e-11 9.247933e-11 8.586619e-11 8.586619e-11
## [8,] 8.275361e-11 8.275361e-11 6.275737e-11 8.274572e-11 8.274572e-11
## [9,] 4.987605e-11 1.356799e-10 4.132104e-11 4.987467e-11 1.356762e-10
## [10,] 1.356799e-10 4.987605e-11 4.132104e-11 1.356762e-10 4.987467e-11
## [11,] NA NA NA NA NA
## [12,] 1.051796e-07 1.051796e-07 1.057554e-07 1.051796e-07 1.051796e-07
## [13,] 8.831306e-11 8.831306e-11 8.832140e-11 8.831306e-11 8.831306e-11
## [14,] 8.713078e-11 8.713078e-11 8.713691e-11 7.747593e-11 7.747593e-11
## [15,] 7.774104e-11 7.774104e-11 7.774151e-11 1.331076e-10 1.331076e-10
## [16,] 1.387095e-10 1.387095e-10 1.387103e-10 1.407247e-10 1.407247e-10
## [17,] 8.850049e-11 8.850049e-11 8.850672e-11 8.882497e-11 8.882497e-11
## [18,] 1.105147e-07 1.105147e-07 1.105147e-07 1.077816e-07 1.077816e-07
## [19,] 6.848663e-11 6.848663e-11 9.845431e-11 6.848009e-11 6.848009e-11
## [,62] [,63]
## [1,] 2.424160e-11 2.402308e-11
## [2,] 2.424160e-11 2.402308e-11
## [3,] 7.942811e-12 7.873889e-12
## [4,] 6.372640e-11 6.317344e-11
## [5,] 1.348236e-11 1.394956e-10
## [6,] 1.348236e-11 1.394956e-10
## [7,] 8.587430e-11 9.268342e-11
## [8,] 6.275138e-11 6.275758e-11
## [9,] 4.131965e-11 4.987610e-11
## [10,] 4.131965e-11 4.987610e-11
## [11,] NA NA
## [12,] 1.057554e-07 1.036337e-07
## [13,] 8.832140e-11 8.829066e-11
## [14,] 7.748138e-11 8.711433e-11
## [15,] 1.331084e-10 1.311993e-10
## [16,] 1.407255e-10 1.387072e-10
## [17,] 8.883121e-11 8.880819e-11
## [18,] 1.077816e-07 1.106125e-07
## [19,] 9.844492e-11 6.848686e-11
##
## $relative_probs_of_each_state_at_branch_top_AT_node_UPPASS
## [,1] [,2] [,3] [,4] [,5] [,6]
## [1,] 0.04713555 0.66685894 0.07731132 0.04721373 0.04706737 0.04706743
## [2,] 0.04713555 0.66685894 0.07731132 0.04721373 0.04706737 0.04706743
## [3,] 0.04848825 0.68885848 0.04846508 0.04851490 0.04846501 0.04846503
## [4,] 0.06225168 0.38884291 0.27996568 0.06246550 0.06206522 0.06206539
## [5,] 0.03979881 0.04030327 0.03956583 0.74141448 0.03954629 0.03954652
## [6,] 0.03979881 0.04030327 0.03956583 0.74141448 0.03954629 0.03954652
## [7,] 0.13929297 0.14198501 0.13935954 0.14121993 0.13928744 0.13928894
## [8,] 0.13240160 0.13239837 0.13240665 0.13240078 0.13240686 0.15885397
## [9,] 0.10370068 0.10369883 0.10370356 0.10370021 0.12441757 0.33679737
## [10,] 0.10370068 0.10369883 0.10370356 0.10370021 0.12441757 0.10370368
## [11,] 0.01587302 0.01587302 0.01587302 0.01587302 0.01587302 0.01587302
## [12,] 0.14001137 0.14001137 0.14001137 0.14001137 0.13986588 0.13990536
## [13,] 0.16707419 0.13548420 0.13548420 0.13548420 0.13537935 0.13540780
## [14,] 0.14150293 0.13870378 0.13870378 0.14472351 0.13869449 0.13869701
## [15,] 0.05452076 0.35418570 0.35418570 0.05529714 0.05384374 0.05384435
## [16,] 0.03526666 0.76931867 0.03484896 0.03574724 0.03484757 0.03484795
## [17,] 0.14076774 0.14463472 0.13898185 0.13883851 0.13883211 0.13883384
## [18,] 0.13994409 0.13992211 0.13997841 0.13993852 0.13997984 0.13997984
## [19,] 0.12859538 0.12858829 0.12860644 0.12859358 0.20812448 0.12860690
## [,7] [,8] [,9] [,10] [,11]
## [1,] 0.04706743 0.0024033849 0.0004218241 0.0003206614 0.0003201695
## [2,] 0.04706743 0.0024033849 0.0004218241 0.0003206614 0.0003201695
## [3,] 0.04846503 0.0024818755 0.0003294140 0.0003295815 0.0003294138
## [4,] 0.06206539 0.0015197377 0.0011537844 0.0004227327 0.0004213873
## [5,] 0.03954652 0.0002727739 0.0002702952 0.0026293148 0.0002702296
## [6,] 0.03954652 0.0002727739 0.0002702952 0.0026293148 0.0002702296
## [7,] 0.13928894 0.0009489577 0.0009401331 0.0009463862 0.0009398908
## [8,] 0.15885397 0.0008935726 0.0008936004 0.0008935807 0.0008936012
## [9,] 0.10370368 0.0007006407 0.0007006566 0.0007006454 0.0007702796
## [10,] 0.33679737 0.0007006407 0.0007006566 0.0007006454 0.0007702796
## [11,] 0.01587302 0.0158730159 0.0158730159 0.0158730159 0.0158730159
## [12,] 0.13990536 0.0009447387 0.0009447387 0.0009447387 0.0009442497
## [13,] 0.13540780 0.0010204845 0.0010204845 0.0010204845 0.0010201321
## [14,] 0.13869701 0.0009453570 0.0009453570 0.0009655903 0.0009453258
## [15,] 0.05384435 0.0013772613 0.0013772613 0.0003726527 0.0003677676
## [16,] 0.03484795 0.0027074689 0.0002391581 0.0002421770 0.0002391534
## [17,] 0.13883384 0.0009628208 0.0009438206 0.0009433388 0.0009433173
## [18,] 0.13997984 0.0009442125 0.0009444018 0.0009442677 0.0009444066
## [19,] 0.12860690 0.0008679730 0.0008680340 0.0008679908 0.0011353065
## [,12] [,13] [,14] [,15] [,16]
## [1,] 0.0003201697 0.0003201697 0.0025048104 0.0024036477 0.0024031558
## [2,] 0.0003201697 0.0003201697 0.0025048104 0.0024036477 0.0024031558
## [3,] 0.0003294139 0.0003294139 0.0024817976 0.0024819650 0.0024817973
## [4,] 0.0004213878 0.0004213878 0.0022515081 0.0015204564 0.0015191110
## [5,] 0.0002702303 0.0002702303 0.0002719908 0.0026310104 0.0002719251
## [6,] 0.0002702303 0.0002702303 0.0002719908 0.0026310104 0.0002719251
## [7,] 0.0009398958 0.0009398958 0.0009491815 0.0009554346 0.0009489391
## [8,] 0.0009824940 0.0009824940 0.0008935896 0.0008935698 0.0008935903
## [9,] 0.0014841210 0.0007006570 0.0007006504 0.0007006392 0.0007702734
## [10,] 0.0007006570 0.0014841210 0.0007006504 0.0007006392 0.0007702734
## [11,] 0.0158730159 0.0158730159 0.0158730159 0.0158730159 0.0158730159
## [12,] 0.0009443824 0.0009443824 0.0009447387 0.0009447387 0.0009442497
## [13,] 0.0010202277 0.0010202277 0.0009143056 0.0009143056 0.0009139532
## [14,] 0.0009453343 0.0009453343 0.0009359486 0.0009561819 0.0009359174
## [15,] 0.0003677696 0.0003677696 0.0023844794 0.0013798708 0.0013749857
## [16,] 0.0002391547 0.0002391547 0.0027060651 0.0027090840 0.0027060605
## [17,] 0.0009433231 0.0009433231 0.0009568181 0.0009563363 0.0009563148
## [18,] 0.0009444066 0.0009444066 0.0009443279 0.0009441938 0.0009443327
## [19,] 0.0008680356 0.0008680356 0.0008680102 0.0008679670 0.0011352826
## [,17] [,18] [,19] [,20] [,21]
## [1,] 0.0024031560 0.0024031560 0.0004220868 0.0004215949 0.0004215951
## [2,] 0.0024031560 0.0024031560 0.0004220868 0.0004215949 0.0004215951
## [3,] 0.0024817974 0.0024817974 0.0003295036 0.0003293359 0.0003293360
## [4,] 0.0015191115 0.0015191115 0.0011545031 0.0011531577 0.0011531583
## [5,] 0.0002719259 0.0002719259 0.0026285317 0.0002694465 0.0002694472
## [6,] 0.0002719259 0.0002719259 0.0026285317 0.0002694465 0.0002694472
## [7,] 0.0009489442 0.0009489442 0.0009466100 0.0009401145 0.0009401196
## [8,] 0.0009824831 0.0009824831 0.0008935977 0.0008936181 0.0009825109
## [9,] 0.0014841148 0.0007006508 0.0007006550 0.0007702893 0.0014841307
## [10,] 0.0007006508 0.0014841148 0.0007006550 0.0007702893 0.0007006667
## [11,] 0.0158730159 0.0158730159 0.0158730159 0.0158730159 0.0158730159
## [12,] 0.0009443824 0.0009443824 0.0009447387 0.0009442497 0.0009443824
## [13,] 0.0009140488 0.0009140488 0.0009143056 0.0009139532 0.0009140488
## [14,] 0.0009359259 0.0009359259 0.0009561819 0.0009359174 0.0009359259
## [15,] 0.0013749877 0.0013749877 0.0013798708 0.0013749857 0.0013749877
## [16,] 0.0027060617 0.0027060617 0.0002407732 0.0002377497 0.0002377509
## [17,] 0.0009563206 0.0009563206 0.0009373361 0.0009373146 0.0009373204
## [18,] 0.0009443327 0.0009443327 0.0009443830 0.0009445219 0.0009445219
## [19,] 0.0008680117 0.0008680117 0.0008680280 0.0011353436 0.0008680727
## [,22] [,23] [,24] [,25] [,26]
## [1,] 0.0004215951 0.0003204322 0.0003204324 0.0003204324 0.0003199405
## [2,] 0.0004215951 0.0003204322 0.0003204324 0.0003204324 0.0003199405
## [3,] 0.0003293360 0.0003295034 0.0003295034 0.0003295034 0.0003293357
## [4,] 0.0011531583 0.0004221059 0.0004221065 0.0004221065 0.0004207611
## [5,] 0.0002694472 0.0026284660 0.0026284668 0.0026284668 0.0002693816
## [6,] 0.0002694472 0.0026284660 0.0026284668 0.0026284668 0.0002693816
## [7,] 0.0009401196 0.0009463676 0.0009463726 0.0009463726 0.0009398772
## [8,] 0.0009825109 0.0008935984 0.0009824912 0.0009824912 0.0009825116
## [9,] 0.0007006667 0.0007702781 0.0014841195 0.0007006555 0.0015537537
## [10,] 0.0014841307 0.0007702781 0.0007006555 0.0014841195 0.0007702897
## [11,] 0.0158730159 0.0158730159 0.0158730159 0.0158730159 0.0158730159
## [12,] 0.0009443824 0.0009442497 0.0009443824 0.0009443824 0.0009438934
## [13,] 0.0009140488 0.0009139532 0.0009140488 0.0009140488 0.0009136964
## [14,] 0.0009359259 0.0009561506 0.0009561591 0.0009561591 0.0009358946
## [15,] 0.0013749877 0.0003703771 0.0003703791 0.0003703791 0.0003654941
## [16,] 0.0002377509 0.0002407685 0.0002407698 0.0002407698 0.0002377463
## [17,] 0.0009373204 0.0009368328 0.0009368387 0.0009368387 0.0009368171
## [18,] 0.0009445219 0.0009443878 0.0009443878 0.0009443878 0.0009445267
## [19,] 0.0008680727 0.0011353004 0.0008680295 0.0008680295 0.0011353452
## [,27] [,28] [,29] [,30] [,31]
## [1,] 0.0003199405 0.0003199407 2.406590e-05 2.314851e-05 2.314405e-05
## [2,] 0.0003199405 0.0003199407 2.406590e-05 2.314851e-05 2.314405e-05
## [3,] 0.0003293357 0.0003293358 2.389844e-05 2.389996e-05 2.389844e-05
## [4,] 0.0004207611 0.0004207617 2.222960e-05 1.560015e-05 1.558795e-05
## [5,] 0.0002693816 0.0002693823 3.594224e-06 2.498664e-05 3.593629e-06
## [6,] 0.0002693816 0.0002693823 3.594224e-06 2.498664e-05 3.593629e-06
## [7,] 0.0009398772 0.0009398823 1.276785e-05 1.282456e-05 1.276566e-05
## [8,] 0.0009825116 0.0010714045 1.205368e-05 1.205350e-05 1.205368e-05
## [9,] 0.0007702897 0.0014841311 9.429222e-06 9.429120e-06 1.006059e-05
## [10,] 0.0015537537 0.0014841311 9.429222e-06 9.429120e-06 1.006059e-05
## [11,] 0.0158730159 0.0158730159 1.587302e-02 1.587302e-02 1.587302e-02
## [12,] 0.0009438934 0.0009440260 1.274946e-05 1.274946e-05 1.274503e-05
## [13,] 0.0009136964 0.0009137921 1.329836e-05 1.329836e-05 1.329517e-05
## [14,] 0.0009358946 0.0009359031 1.271521e-05 1.289870e-05 1.271493e-05
## [15,] 0.0003654941 0.0003654961 2.319969e-05 1.408956e-05 1.404526e-05
## [16,] 0.0002377463 0.0002377475 2.552193e-05 2.554930e-05 2.552189e-05
## [17,] 0.0009368171 0.0009368230 1.288206e-05 1.287769e-05 1.287749e-05
## [18,] 0.0009445267 0.0009445267 1.274369e-05 1.274247e-05 1.274373e-05
## [19,] 0.0011353452 0.0008680743 1.170570e-05 1.170531e-05 1.412942e-05
## [,32] [,33] [,34] [,35] [,36]
## [1,] 2.314406e-05 2.314406e-05 5.178988e-06 5.174527e-06 5.174529e-06
## [2,] 2.314406e-05 2.314406e-05 5.178988e-06 5.174527e-06 5.174529e-06
## [3,] 2.389844e-05 2.389844e-05 4.380640e-06 4.379119e-06 4.379120e-06
## [4,] 1.558796e-05 1.558796e-05 1.228155e-05 1.226935e-05 1.226936e-05
## [5,] 3.593636e-06 3.593636e-06 2.496417e-05 3.571151e-06 3.571158e-06
## [6,] 3.593636e-06 3.593636e-06 2.496417e-05 3.571151e-06 3.571158e-06
## [7,] 1.276570e-05 1.276570e-05 1.274453e-05 1.268563e-05 1.268568e-05
## [8,] 1.285979e-05 1.285979e-05 1.205375e-05 1.205393e-05 1.286005e-05
## [9,] 1.653397e-05 9.429225e-06 9.429264e-06 1.006073e-05 1.653411e-05
## [10,] 9.429225e-06 1.653397e-05 9.429264e-06 1.006073e-05 9.429369e-06
## [11,] 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02
## [12,] 1.274623e-05 1.274623e-05 1.274946e-05 1.274503e-05 1.274623e-05
## [13,] 1.329603e-05 1.329603e-05 1.329836e-05 1.329517e-05 1.329603e-05
## [14,] 1.271501e-05 1.271501e-05 1.289870e-05 1.271493e-05 1.271501e-05
## [15,] 1.404528e-05 1.404528e-05 1.408956e-05 1.404526e-05 1.404528e-05
## [16,] 2.552190e-05 2.552190e-05 3.171825e-06 3.144414e-06 3.144425e-06
## [17,] 1.287755e-05 1.287755e-05 1.270539e-05 1.270519e-05 1.270524e-05
## [18,] 1.274373e-05 1.274373e-05 1.274419e-05 1.274544e-05 1.274544e-05
## [19,] 1.170571e-05 1.170571e-05 1.170586e-05 1.412998e-05 1.170626e-05
## [,37] [,38] [,39] [,40] [,41]
## [1,] 5.174529e-06 4.257146e-06 4.257148e-06 4.257148e-06 4.252687e-06
## [2,] 5.174529e-06 4.257146e-06 4.257148e-06 4.257148e-06 4.252687e-06
## [3,] 4.379120e-06 4.380637e-06 4.380638e-06 4.380638e-06 4.379117e-06
## [4,] 1.226936e-05 5.639904e-06 5.639909e-06 5.639909e-06 5.627708e-06
## [5,] 3.571158e-06 2.496357e-05 2.496358e-05 2.496358e-05 3.570563e-06
## [6,] 3.571158e-06 2.496357e-05 2.496358e-05 2.496358e-05 3.570563e-06
## [7,] 1.268568e-05 1.274234e-05 1.274238e-05 1.274238e-05 1.268348e-05
## [8,] 1.286005e-05 1.205376e-05 1.285987e-05 1.285987e-05 1.286005e-05
## [9,] 9.429369e-06 1.006063e-05 1.653401e-05 9.429267e-06 1.716548e-05
## [10,] 1.653411e-05 1.006063e-05 9.429267e-06 1.653401e-05 1.006074e-05
## [11,] 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02
## [12,] 1.274623e-05 1.274503e-05 1.274623e-05 1.274623e-05 1.274180e-05
## [13,] 1.329603e-05 1.329517e-05 1.329603e-05 1.329603e-05 1.329284e-05
## [14,] 1.271501e-05 1.289841e-05 1.289849e-05 1.289849e-05 1.271472e-05
## [15,] 1.404528e-05 4.935137e-06 4.935156e-06 4.935156e-06 4.890856e-06
## [16,] 3.144425e-06 3.171783e-06 3.171795e-06 3.171795e-06 3.144383e-06
## [17,] 1.270524e-05 1.270082e-05 1.270088e-05 1.270088e-05 1.270068e-05
## [18,] 1.274544e-05 1.274423e-05 1.274423e-05 1.274423e-05 1.274549e-05
## [19,] 1.170626e-05 1.412958e-05 1.170587e-05 1.170587e-05 1.412999e-05
## [,42] [,43] [,44] [,45] [,46]
## [1,] 4.252687e-06 4.252689e-06 2.406828e-05 2.406382e-05 2.406382e-05
## [2,] 4.252687e-06 4.252689e-06 2.406828e-05 2.406382e-05 2.406382e-05
## [3,] 4.379117e-06 4.379118e-06 2.389925e-05 2.389773e-05 2.389773e-05
## [4,] 5.627708e-06 5.627713e-06 2.223612e-05 2.222392e-05 2.222392e-05
## [5,] 3.570563e-06 3.570570e-06 2.497954e-05 3.586527e-06 3.586534e-06
## [6,] 3.570563e-06 3.570570e-06 2.497954e-05 3.586527e-06 3.586534e-06
## [7,] 1.268348e-05 1.268352e-05 1.282659e-05 1.276768e-05 1.276773e-05
## [8,] 1.286005e-05 1.366617e-05 1.205365e-05 1.205384e-05 1.285995e-05
## [9,] 1.006074e-05 1.653411e-05 9.429207e-06 1.006068e-05 1.653405e-05
## [10,] 1.716548e-05 1.653411e-05 9.429207e-06 1.006068e-05 9.429313e-06
## [11,] 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02
## [12,] 1.274180e-05 1.274300e-05 1.274946e-05 1.274503e-05 1.274623e-05
## [13,] 1.329284e-05 1.329371e-05 1.233549e-05 1.233230e-05 1.233317e-05
## [14,] 1.271472e-05 1.271480e-05 1.281338e-05 1.262961e-05 1.262969e-05
## [15,] 4.890856e-06 4.890875e-06 2.322335e-05 2.317905e-05 2.317907e-05
## [16,] 3.144383e-06 3.144395e-06 2.553657e-05 2.550916e-05 2.550917e-05
## [17,] 1.270068e-05 1.270073e-05 1.282325e-05 1.282306e-05 1.282311e-05
## [18,] 1.274549e-05 1.274549e-05 1.274352e-05 1.274477e-05 1.274477e-05
## [19,] 1.412999e-05 1.170628e-05 1.170564e-05 1.412976e-05 1.170605e-05
## [,47] [,48] [,49] [,50] [,51]
## [1,] 2.406382e-05 2.314644e-05 2.314644e-05 2.314644e-05 2.314198e-05
## [2,] 2.406382e-05 2.314644e-05 2.314644e-05 2.314644e-05 2.314198e-05
## [3,] 2.389773e-05 2.389925e-05 2.389925e-05 2.389925e-05 2.389773e-05
## [4,] 2.222392e-05 1.559447e-05 1.559447e-05 1.559447e-05 1.558227e-05
## [5,] 3.586534e-06 2.497895e-05 2.497895e-05 2.497895e-05 3.585939e-06
## [6,] 3.586534e-06 2.497895e-05 2.497895e-05 2.497895e-05 3.585939e-06
## [7,] 1.276773e-05 1.282439e-05 1.282444e-05 1.282444e-05 1.276553e-05
## [8,] 1.285995e-05 1.205366e-05 1.285977e-05 1.285977e-05 1.285995e-05
## [9,] 9.429313e-06 1.006057e-05 1.653395e-05 9.429211e-06 1.716542e-05
## [10,] 1.653405e-05 1.006057e-05 9.429211e-06 1.653395e-05 1.006068e-05
## [11,] 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02
## [12,] 1.274623e-05 1.274503e-05 1.274623e-05 1.274623e-05 1.274180e-05
## [13,] 1.233317e-05 1.233230e-05 1.233317e-05 1.233317e-05 1.232997e-05
## [14,] 1.262969e-05 1.281309e-05 1.281317e-05 1.281317e-05 1.262940e-05
## [15,] 2.317907e-05 1.406893e-05 1.406895e-05 1.406895e-05 1.402465e-05
## [16,] 2.550917e-05 2.553653e-05 2.553654e-05 2.553654e-05 2.550913e-05
## [17,] 1.282311e-05 1.281869e-05 1.281874e-05 1.281874e-05 1.281855e-05
## [18,] 1.274477e-05 1.274356e-05 1.274356e-05 1.274356e-05 1.274482e-05
## [19,] 1.170605e-05 1.412937e-05 1.170566e-05 1.170566e-05 1.412977e-05
## [,52] [,53] [,54] [,55] [,56]
## [1,] 2.314198e-05 2.314198e-05 5.176910e-06 5.176912e-06 5.176912e-06
## [2,] 2.314198e-05 2.314198e-05 5.176910e-06 5.176912e-06 5.176912e-06
## [3,] 2.389773e-05 2.389773e-05 4.379931e-06 4.379932e-06 4.379932e-06
## [4,] 1.558227e-05 1.558228e-05 1.227587e-05 1.227587e-05 1.227587e-05
## [5,] 3.585939e-06 3.585946e-06 2.495647e-05 2.495648e-05 2.495648e-05
## [6,] 3.585939e-06 3.585946e-06 2.495647e-05 2.495648e-05 2.495648e-05
## [7,] 1.276553e-05 1.276558e-05 1.274437e-05 1.274441e-05 1.274441e-05
## [8,] 1.285995e-05 1.366607e-05 1.205391e-05 1.286002e-05 1.286002e-05
## [9,] 1.006068e-05 1.653406e-05 1.006072e-05 1.653410e-05 9.429355e-06
## [10,] 1.716542e-05 1.653406e-05 1.006072e-05 9.429355e-06 1.653410e-05
## [11,] 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02
## [12,] 1.274180e-05 1.274300e-05 1.274503e-05 1.274623e-05 1.274623e-05
## [13,] 1.232997e-05 1.233084e-05 1.233230e-05 1.233317e-05 1.233317e-05
## [14,] 1.262940e-05 1.262948e-05 1.281309e-05 1.281317e-05 1.281317e-05
## [15,] 1.402465e-05 1.402466e-05 1.406893e-05 1.406895e-05 1.406895e-05
## [16,] 2.550913e-05 2.550914e-05 3.159057e-06 3.159068e-06 3.159068e-06
## [17,] 1.281855e-05 1.281860e-05 1.264639e-05 1.264644e-05 1.264644e-05
## [18,] 1.274482e-05 1.274482e-05 1.274527e-05 1.274527e-05 1.274527e-05
## [19,] 1.412977e-05 1.170606e-05 1.412992e-05 1.170621e-05 1.170621e-05
## [,57] [,58] [,59] [,60] [,61]
## [1,] 5.172451e-06 5.172451e-06 5.172453e-06 4.255070e-06 4.255070e-06
## [2,] 5.172451e-06 5.172451e-06 5.172453e-06 4.255070e-06 4.255070e-06
## [3,] 4.378411e-06 4.378411e-06 4.378412e-06 4.379929e-06 4.379929e-06
## [4,] 1.226367e-05 1.226367e-05 1.226368e-05 5.634226e-06 5.634226e-06
## [5,] 3.563462e-06 3.563462e-06 3.563468e-06 2.495588e-05 2.495588e-05
## [6,] 3.563462e-06 3.563462e-06 3.563468e-06 2.495588e-05 2.495588e-05
## [7,] 1.268551e-05 1.268551e-05 1.268555e-05 1.274221e-05 1.274221e-05
## [8,] 1.286021e-05 1.286021e-05 1.366632e-05 1.286003e-05 1.286003e-05
## [9,] 1.716557e-05 1.006082e-05 1.653420e-05 1.716546e-05 1.006072e-05
## [10,] 1.006082e-05 1.716557e-05 1.653420e-05 1.006072e-05 1.716546e-05
## [11,] 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02 1.587302e-02
## [12,] 1.274180e-05 1.274180e-05 1.274300e-05 1.274180e-05 1.274180e-05
## [13,] 1.232997e-05 1.232997e-05 1.233084e-05 1.232997e-05 1.232997e-05
## [14,] 1.262940e-05 1.262940e-05 1.262948e-05 1.281289e-05 1.281289e-05
## [15,] 1.402465e-05 1.402465e-05 1.402466e-05 4.914520e-06 4.914520e-06
## [16,] 3.131656e-06 3.131656e-06 3.131668e-06 3.159026e-06 3.159026e-06
## [17,] 1.264625e-05 1.264625e-05 1.264630e-05 1.264188e-05 1.264188e-05
## [18,] 1.274653e-05 1.274653e-05 1.274653e-05 1.274532e-05 1.274532e-05
## [19,] 1.413033e-05 1.413033e-05 1.170662e-05 1.412994e-05 1.412994e-05
## [,62] [,63]
## [1,] 4.255072e-06 4.250611e-06
## [2,] 4.255072e-06 4.250611e-06
## [3,] 4.379930e-06 4.378409e-06
## [4,] 5.634231e-06 5.622030e-06
## [5,] 2.495589e-05 3.562873e-06
## [6,] 2.495589e-05 3.562873e-06
## [7,] 1.274226e-05 1.268336e-05
## [8,] 1.366614e-05 1.366633e-05
## [9,] 1.653410e-05 1.716557e-05
## [10,] 1.653410e-05 1.716557e-05
## [11,] 1.587302e-02 1.587302e-02
## [12,] 1.274300e-05 1.273856e-05
## [13,] 1.233084e-05 1.232764e-05
## [14,] 1.281296e-05 1.262920e-05
## [15,] 4.914539e-06 4.870239e-06
## [16,] 3.159037e-06 3.131626e-06
## [17,] 1.264193e-05 1.264173e-05
## [18,] 1.274532e-05 1.274658e-05
## [19,] 1.170622e-05 1.413034e-05
##
## $ML_marginal_prob_each_state_at_branch_bottom_below_node
## [,1] [,2] [,3] [,4] [,5]
## [1,] 0.0005806179 0.993885248 0.0032082502 0.0005874256 0.0005746814
## [2,] 0.0005806179 0.993885248 0.0032082502 0.0005874256 0.0005746814
## [3,] 0.0043493080 0.910787132 0.0672385849 0.0043870240 0.0043164187
## [4,] 0.0029664612 0.943559760 0.0413799295 0.0030041772 0.0029335718
## [5,] 0.0006349755 0.000651163 0.0006274995 0.9961943615 0.0006268727
## [6,] 0.0006349755 0.000651163 0.0006274995 0.9961943615 0.0006268727
## [7,] 0.1609124954 0.183139134 0.1236850470 0.1658138702 0.1220522301
## [8,] 0.0883317673 0.088318116 0.0883530780 0.0883283041 0.2464303708
## [9,] 0.0464518494 0.046449352 0.0464557473 0.0464512159 0.0744790810
## [10,] 0.0464518494 0.046449352 0.0464557473 0.0464512159 0.0744790810
## [11,] NA NA NA NA NA
## [12,] 0.1075227537 0.113453217 0.0982649398 0.1090272645 0.0979832629
## [13,] 0.1596521877 0.184439485 0.1234874855 0.1666777207 0.1218168080
## [14,] 0.1455332473 0.202289549 0.1203853483 0.1768623082 0.1182181789
## [15,] 0.0026002697 0.962497108 0.0245263565 0.0026570607 0.0025507463
## [16,] 0.0027590517 0.958122213 0.0281102580 0.0028176515 0.0027079509
## [17,] 0.1456304785 0.200227919 0.1204193721 0.1785312780 0.1183053081
## [18,] 0.1002897639 0.100364933 0.1001724199 0.1003088338 0.1085195493
## [19,] 0.0880897643 0.088076132 0.0881110455 0.0880863058 0.2411241125
## [,6] [,7] [,8] [,9] [,10]
## [1,] 0.0005746867 0.0005746867 1.075138e-06 6.819333e-07 4.062455e-07
## [2,] 0.0005746867 0.0005746867 1.075138e-06 6.819333e-07 4.062455e-07
## [3,] 0.0043164482 0.0043164482 1.633807e-06 4.295154e-05 5.241329e-06
## [4,] 0.0029336014 0.0029336014 5.247361e-05 4.869159e-07 1.079554e-06
## [5,] 0.0006268800 0.0006268800 4.008648e-07 3.956095e-07 9.053947e-07
## [6,] 0.0006268800 0.0006268800 4.008648e-07 3.956095e-07 9.053947e-07
## [7,] 0.1220862221 0.1220862221 1.130974e-05 1.236073e-05 1.161600e-05
## [8,] 0.1999999580 0.1999999580 9.942971e-06 9.944136e-06 9.943310e-06
## [9,] 0.3618514988 0.3775404550 8.359574e-06 8.359930e-06 8.359678e-06
## [10,] 0.3775404550 0.3618514988 8.359574e-06 8.359930e-06 8.359678e-06
## [11,] NA NA NA NA NA
## [12,] 0.0979551922 0.0979551922 1.432840e-02 1.334702e-02 1.404242e-02
## [13,] 0.1218507671 0.1218507671 1.139832e-05 9.138346e-06 1.073975e-05
## [14,] 0.1182426977 0.1182426977 1.414536e-05 1.054264e-05 9.487438e-06
## [15,] 0.0025507907 0.0025507907 1.040119e-05 5.288411e-07 8.855247e-07
## [16,] 0.0027079968 0.0027079968 1.026074e-06 8.850164e-06 1.595210e-06
## [17,] 0.1183298360 0.1183298360 9.519641e-06 1.083321e-05 1.361510e-05
## [18,] 0.1062531611 0.1062531611 1.248549e-02 1.286405e-02 1.259581e-02
## [19,] 0.2031370961 0.2031370961 8.873301e-06 8.874321e-06 8.873598e-06
## [,11] [,12] [,13] [,14] [,15]
## [1,] 4.049049e-07 4.049055e-07 4.049055e-07 1.570482e-06 1.076421e-06
## [2,] 4.049049e-07 4.049055e-07 4.049055e-07 1.570482e-06 1.076421e-06
## [3,] 5.234810e-06 5.234813e-06 5.234813e-06 1.339998e-05 1.634557e-06
## [4,] 1.073035e-06 1.073037e-06 1.073037e-06 1.339998e-05 5.250218e-05
## [5,] 3.954703e-07 3.954719e-07 3.954719e-07 3.992045e-07 9.121113e-07
## [6,] 3.954703e-07 3.954719e-07 3.954719e-07 3.992045e-07 9.121113e-07
## [7,] 1.238379e-05 1.238476e-05 1.238476e-05 9.744454e-06 9.101286e-06
## [8,] 1.879804e-05 8.238504e-06 8.238504e-06 9.943681e-06 9.942856e-06
## [9,] 9.923646e-06 3.529255e-06 3.792555e-05 8.359791e-06 8.359538e-06
## [10,] 9.923646e-06 3.792555e-05 3.529255e-06 8.359791e-06 8.359538e-06
## [11,] NA NA NA NA NA
## [12,] 1.310872e-02 1.316663e-02 1.316663e-02 1.373021e-02 1.442561e-02
## [13,] 9.078509e-06 9.079196e-06 9.079196e-06 1.218210e-05 1.388505e-05
## [14,] 1.044923e-05 1.044979e-05 1.044979e-05 1.339150e-05 1.209558e-05
## [15,] 8.734251e-07 8.734302e-07 8.734302e-07 3.604148e-06 1.047593e-05
## [16,] 1.572984e-06 1.572993e-06 1.572993e-06 1.861177e-06 1.032406e-06
## [17,] 1.086436e-05 1.086495e-05 1.086495e-05 8.935771e-06 1.123469e-05
## [18,] 1.340829e-02 1.326321e-02 1.326321e-02 1.271624e-02 1.244799e-02
## [19,] 6.535691e-06 1.463707e-05 1.463707e-05 8.873923e-06 8.873200e-06
## [,16] [,17] [,18] [,19] [,20]
## [1,] 1.074019e-06 1.074020e-06 1.074020e-06 6.826494e-07 6.813088e-07
## [2,] 1.074019e-06 1.074020e-06 1.074020e-06 6.826494e-07 6.813088e-07
## [3,] 1.633153e-06 1.633153e-06 1.633153e-06 4.298011e-05 4.292662e-05
## [4,] 5.244869e-05 5.244871e-05 5.244871e-05 4.876664e-07 4.862615e-07
## [5,] 3.990653e-07 3.990669e-07 3.990669e-07 9.022928e-07 3.938100e-07
## [6,] 3.990653e-07 3.990669e-07 3.990669e-07 9.022928e-07 3.938100e-07
## [7,] 9.764698e-06 9.765450e-06 9.765450e-06 1.000895e-05 1.067205e-05
## [8,] 1.879718e-05 8.238139e-06 8.238139e-06 9.944020e-06 1.879938e-05
## [9,] 9.923507e-06 3.529205e-06 3.792492e-05 8.359895e-06 9.923864e-06
## [10,] 9.923507e-06 3.792492e-05 3.529205e-06 8.359895e-06 9.923864e-06
## [11,] NA NA NA NA NA
## [12,] 1.348577e-02 1.354535e-02 1.354535e-02 1.344423e-02 1.252011e-02
## [13,] 1.211773e-05 1.211866e-05 1.211866e-05 1.148176e-05 9.715118e-06
## [14,] 1.330278e-05 1.330354e-05 1.330354e-05 9.014927e-06 9.914660e-06
## [15,] 1.033602e-05 1.033608e-05 1.033608e-05 5.326412e-07 5.255273e-07
## [16,] 1.020553e-06 1.020558e-06 1.020558e-06 8.916964e-06 8.791913e-06
## [17,] 8.964830e-06 8.965328e-06 8.965328e-06 1.276123e-05 1.018288e-05
## [18,] 1.325433e-02 1.311092e-02 1.311092e-02 1.282655e-02 1.364862e-02
## [19,] 6.535415e-06 1.463641e-05 1.463641e-05 8.874220e-06 6.536121e-06
## [,21] [,22] [,23] [,24] [,25]
## [1,] 6.813094e-07 6.813094e-07 4.056210e-07 4.056216e-07 4.056216e-07
## [2,] 6.813094e-07 6.813094e-07 4.056210e-07 4.056216e-07 4.056216e-07
## [3,] 4.292664e-05 4.292664e-05 5.238292e-06 5.238295e-06 5.238295e-06
## [4,] 4.862621e-07 4.862621e-07 1.076517e-06 1.076520e-06 1.076520e-06
## [5,] 3.938116e-07 3.938116e-07 9.020327e-07 9.020357e-07 9.020357e-07
## [6,] 3.938116e-07 3.938116e-07 9.020327e-07 9.020357e-07 9.020357e-07
## [7,] 1.067289e-05 1.067289e-05 1.002911e-05 1.002988e-05 1.002988e-05
## [8,] 8.239074e-06 8.239074e-06 1.879782e-05 8.238412e-06 8.238412e-06
## [9,] 3.529334e-06 3.792654e-05 9.923611e-06 3.529243e-06 3.792539e-05
## [10,] 3.792654e-05 3.529334e-06 9.923611e-06 3.792539e-05 3.529243e-06
## [11,] NA NA NA NA NA
## [12,] 1.257542e-02 1.257542e-02 1.320437e-02 1.326271e-02 1.326271e-02
## [13,] 9.715865e-06 9.715865e-06 1.141759e-05 1.141847e-05 1.141847e-05
## [14,] 9.915224e-06 9.915224e-06 8.934985e-06 8.935481e-06 8.935481e-06
## [15,] 5.255302e-07 5.255302e-07 8.798885e-07 8.798935e-07 8.798935e-07
## [16,] 8.791965e-06 8.791965e-06 1.584857e-06 1.584866e-06 1.584866e-06
## [17,] 1.018347e-05 1.018347e-05 1.279724e-05 1.279797e-05 1.279797e-05
## [18,] 1.350094e-02 1.350094e-02 1.336923e-02 1.322458e-02 1.322458e-02
## [19,] 1.463809e-05 1.463809e-05 6.535621e-06 1.463690e-05 1.463690e-05
## [,26] [,27] [,28] [,29] [,30]
## [1,] 4.042810e-07 4.042810e-07 4.042816e-07 9.271669e-12 5.630841e-12
## [2,] 4.042810e-07 4.042810e-07 4.042816e-07 9.271669e-12 5.630841e-12
## [3,] 5.231776e-06 5.231776e-06 5.231778e-06 7.920609e-11 1.338891e-11
## [4,] 1.070000e-06 1.070000e-06 1.070003e-06 7.920609e-11 3.533166e-10
## [5,] 3.936724e-07 3.936724e-07 3.936740e-07 3.736145e-12 5.568064e-12
## [6,] 3.936724e-07 3.936724e-07 3.936740e-07 3.736145e-12 5.568064e-12
## [7,] 1.069280e-05 1.069280e-05 1.069364e-05 8.819731e-11 8.117206e-11
## [8,] 1.557485e-05 1.557485e-05 6.533291e-06 8.639067e-11 8.638243e-11
## [9,] 4.091811e-06 4.502046e-05 1.601113e-05 7.484663e-11 7.484412e-11
## [10,] 4.502046e-05 4.091811e-06 1.601113e-05 7.484663e-11 7.484412e-11
## [11,] NA NA NA NA NA
## [12,] 1.234739e-02 1.234739e-02 1.240260e-02 1.123218e-07 1.161237e-07
## [13,] 9.652205e-06 9.652205e-06 9.652947e-06 8.587120e-11 9.453353e-11
## [14,] 9.827248e-06 9.827248e-06 9.827807e-06 1.067588e-10 9.448028e-11
## [15,] 8.677940e-07 8.677940e-07 8.677990e-07 2.087457e-11 6.780005e-11
## [16,] 1.562640e-06 1.562640e-06 1.562649e-06 1.153472e-11 6.639016e-12
## [17,] 1.021220e-05 1.021220e-05 1.021278e-05 7.638641e-11 8.976186e-11
## [18,] 1.405544e-02 1.405544e-02 1.390766e-02 1.011325e-07 9.847757e-08
## [19,] 1.078050e-05 1.078050e-05 2.040128e-05 7.566328e-11 7.565606e-11
## [,31] [,32] [,33] [,34] [,35]
## [1,] 5.613137e-12 5.613144e-12 5.613144e-12 4.172840e-12 4.159720e-12
## [2,] 5.613137e-12 5.613144e-12 5.613144e-12 4.172840e-12 4.159720e-12
## [3,] 1.337454e-11 1.337455e-11 1.337455e-11 4.386260e-11 4.348353e-11
## [4,] 3.529375e-10 3.529377e-10 3.529377e-10 1.662170e-12 1.647805e-12
## [5,] 3.734821e-12 3.734837e-12 3.734837e-12 5.493564e-12 3.684849e-12
## [6,] 3.734821e-12 3.734837e-12 3.734837e-12 5.493564e-12 3.684849e-12
## [7,] 8.841794e-11 8.842629e-11 8.842629e-11 9.108641e-11 9.832884e-11
## [8,] 1.381830e-10 6.957834e-11 6.957834e-11 8.639406e-11 1.382017e-10
## [9,] 9.034401e-11 2.751371e-11 2.541599e-10 7.484766e-11 9.034754e-11
## [10,] 9.034401e-11 2.541599e-10 2.751371e-11 7.484766e-11 9.034754e-11
## [11,] NA NA NA NA NA
## [12,] 1.099990e-07 1.105924e-07 1.105924e-07 1.107582e-07 1.047381e-07
## [13,] 8.553146e-11 8.553954e-11 8.553954e-11 8.230886e-11 7.331105e-11
## [14,] 1.062286e-10 1.062356e-10 1.062356e-10 7.678361e-11 8.633143e-11
## [15,] 6.683411e-11 6.683451e-11 6.683451e-11 4.808438e-12 4.739933e-12
## [16,] 6.544431e-12 6.544471e-12 6.544471e-12 6.360518e-11 6.269901e-11
## [17,] 7.669679e-11 7.670179e-11 7.670179e-11 1.049346e-10 8.966108e-11
## [18,] 1.040531e-07 1.032863e-07 1.032863e-07 1.022244e-07 1.079045e-07
## [19,] 5.263295e-11 1.087776e-10 1.087776e-10 7.566625e-11 5.264004e-11
## [,36] [,37] [,38] [,39] [,40]
## [1,] 4.159726e-12 4.159726e-12 1.461617e-12 1.461622e-12 1.461622e-12
## [2,] 4.159726e-12 4.159726e-12 1.461617e-12 1.461622e-12 1.461622e-12
## [3,] 4.348369e-11 4.348369e-11 7.406442e-12 7.406469e-12 7.406469e-12
## [4,] 1.647811e-12 1.647811e-12 7.406442e-12 7.406469e-12 7.406469e-12
## [5,] 3.684865e-12 3.684865e-12 5.491591e-12 5.491614e-12 5.491614e-12
## [6,] 3.684865e-12 3.684865e-12 5.491591e-12 5.491614e-12 5.491614e-12
## [7,] 9.833812e-11 9.833812e-11 9.130603e-11 9.131465e-11 9.131465e-11
## [8,] 6.958771e-11 6.958771e-11 1.381885e-10 6.958107e-11 6.958107e-11
## [9,] 2.751501e-11 2.541720e-10 9.034504e-11 2.751409e-11 2.541634e-10
## [10,] 2.541720e-10 2.751501e-11 9.034504e-11 2.541634e-10 2.751409e-11
## [11,] NA NA NA NA NA
## [12,] 1.053031e-07 1.053031e-07 1.084659e-07 1.090511e-07 1.090511e-07
## [13,] 7.331797e-11 7.331797e-11 8.197036e-11 8.197810e-11 8.197810e-11
## [14,] 8.633706e-11 8.633706e-11 7.631654e-11 7.632151e-11 7.632151e-11
## [15,] 4.739962e-12 4.739962e-12 8.114893e-12 8.114941e-12 8.114941e-12
## [16,] 6.269939e-11 6.269939e-11 1.523184e-11 1.523193e-11 1.523193e-11
## [17,] 8.966693e-11 8.966693e-11 1.052940e-10 1.053009e-10 1.053009e-10
## [18,] 1.071093e-07 1.071093e-07 1.051754e-07 1.044004e-07 1.044004e-07
## [19,] 1.087922e-10 1.087922e-10 5.263502e-11 1.087819e-10 1.087819e-10
## [,41] [,42] [,43] [,44] [,45]
## [1,] 1.448502e-12 1.448502e-12 1.448508e-12 9.281126e-12 9.263422e-12
## [2,] 1.448502e-12 1.448502e-12 1.448508e-12 9.281126e-12 9.263422e-12
## [3,] 7.342460e-12 7.342460e-12 7.342486e-12 7.925153e-11 7.916646e-11
## [4,] 7.342460e-12 7.342460e-12 7.342486e-12 7.925153e-11 7.916646e-11
## [5,] 3.683541e-12 3.683541e-12 3.683556e-12 5.544527e-12 3.719034e-12
## [6,] 3.683541e-12 3.683541e-12 3.683556e-12 5.544527e-12 3.719034e-12
## [7,] 9.855515e-11 9.855515e-11 9.856446e-11 7.315581e-11 7.970648e-11
## [8,] 1.113065e-10 1.113065e-10 5.277300e-11 8.638952e-11 1.381944e-10
## [9,] 3.321186e-11 3.067970e-10 9.343392e-11 7.484628e-11 9.034616e-11
## [10,] 3.067970e-10 3.321186e-11 9.343392e-11 7.484628e-11 9.034616e-11
## [11,] NA NA NA NA NA
## [12,] 1.030895e-07 1.030895e-07 1.036538e-07 1.128533e-07 1.067923e-07
## [13,] 7.298267e-11 7.298267e-11 7.298957e-11 1.022244e-10 9.252165e-11
## [14,] 8.581187e-11 8.581187e-11 8.581747e-11 8.805566e-11 9.900328e-11
## [15,] 7.999327e-12 7.999327e-12 7.999375e-12 2.103573e-11 2.073404e-11
## [16,] 1.501492e-11 1.501492e-11 1.501501e-11 1.162377e-11 1.145706e-11
## [17,] 8.997405e-11 8.997405e-11 8.997992e-11 8.290577e-11 7.083729e-11
## [18,] 1.101391e-07 1.101391e-07 1.093432e-07 1.007614e-07 1.064006e-07
## [19,] 7.567813e-11 7.567813e-11 1.419112e-10 7.566227e-11 5.263727e-11
## [,46] [,47] [,48] [,49] [,50]
## [1,] 9.263429e-12 9.263429e-12 5.622594e-12 5.622602e-12 5.622602e-12
## [2,] 9.263429e-12 9.263429e-12 5.622594e-12 5.622602e-12 5.622602e-12
## [3,] 7.916650e-11 7.916650e-11 1.338221e-11 1.338222e-11 1.338222e-11
## [4,] 7.916650e-11 7.916650e-11 3.531400e-10 3.531402e-10 3.531402e-10
## [5,] 3.719049e-12 3.719049e-12 5.542554e-12 5.542577e-12 5.542577e-12
## [6,] 3.719049e-12 3.719049e-12 5.542554e-12 5.542577e-12 5.542577e-12
## [7,] 7.971401e-11 7.971401e-11 7.335756e-11 7.336449e-11 7.336449e-11
## [8,] 6.958405e-11 6.958405e-11 1.381812e-10 6.957741e-11 6.957741e-11
## [9,] 2.751450e-11 2.541673e-10 9.034366e-11 2.751358e-11 2.541588e-10
## [10,] 2.541673e-10 2.751450e-11 9.034366e-11 2.541588e-10 2.751358e-11
## [11,] NA NA NA NA NA
## [12,] 1.073684e-07 1.073684e-07 1.105201e-07 1.111163e-07 1.111163e-07
## [13,] 9.253039e-11 9.253039e-11 1.018549e-10 1.018645e-10 1.018645e-10
## [14,] 9.901024e-11 9.901024e-11 8.761672e-11 8.762288e-11 8.762288e-11
## [15,] 2.073416e-11 2.073416e-11 6.735009e-11 6.735050e-11 6.735050e-11
## [16,] 1.145713e-11 1.145713e-11 6.594957e-12 6.594996e-12 6.594996e-12
## [17,] 7.084227e-11 7.084227e-11 8.324108e-11 8.324693e-11 8.324693e-11
## [18,] 1.056166e-07 1.056166e-07 1.036716e-07 1.029077e-07 1.029077e-07
## [19,] 1.087865e-10 1.087865e-10 5.263225e-11 1.087761e-10 1.087761e-10
## [,51] [,52] [,53] [,54] [,55]
## [1,] 5.604897e-12 5.604897e-12 5.604905e-12 4.166729e-12 4.166734e-12
## [2,] 5.604897e-12 5.604897e-12 5.604905e-12 4.166729e-12 4.166734e-12
## [3,] 1.336786e-11 1.336786e-11 1.336786e-11 4.368602e-11 4.368618e-11
## [4,] 3.527611e-10 3.527611e-10 3.527613e-10 1.655478e-12 1.655484e-12
## [5,] 3.717725e-12 3.717725e-12 3.717741e-12 5.468054e-12 5.468077e-12
## [6,] 3.717725e-12 3.717725e-12 3.717741e-12 5.468054e-12 5.468077e-12
## [7,] 7.991341e-11 7.991341e-11 7.992096e-11 8.231745e-11 8.232522e-11
## [8,] 1.113006e-10 1.113006e-10 5.277023e-11 1.381998e-10 6.958678e-11
## [9,] 3.321135e-11 3.067923e-10 9.343219e-11 9.034719e-11 2.751488e-11
## [10,] 3.067923e-10 3.321135e-11 9.343219e-11 9.034719e-11 2.541708e-10
## [11,] NA NA NA NA NA
## [12,] 1.051139e-07 1.051139e-07 1.056893e-07 1.052592e-07 1.058271e-07
## [13,] 9.216430e-11 9.216430e-11 9.217300e-11 8.868342e-11 8.869180e-11
## [14,] 9.851669e-11 9.851669e-11 9.852362e-11 7.120563e-11 7.121064e-11
## [15,] 6.638456e-11 6.638456e-11 6.638497e-11 4.776527e-12 4.776556e-12
## [16,] 6.500411e-12 6.500411e-12 6.500451e-12 6.318307e-11 6.318345e-11
## [17,] 7.112878e-11 7.112878e-11 7.113378e-11 9.731157e-11 9.731841e-11
## [18,] 1.086055e-07 1.086055e-07 1.078208e-07 1.075230e-07 1.067306e-07
## [19,] 7.567415e-11 7.567415e-11 1.419038e-10 5.263934e-11 1.087908e-10
## [,56] [,57] [,58] [,59] [,60]
## [1,] 4.166734e-12 4.153614e-12 4.153614e-12 4.153620e-12 1.455511e-12
## [2,] 4.166734e-12 4.153614e-12 4.153614e-12 4.153620e-12 1.455511e-12
## [3,] 4.368618e-11 4.330711e-11 4.330711e-11 4.330727e-11 7.376652e-12
## [4,] 1.655484e-12 1.641120e-12 1.641120e-12 1.641126e-12 7.376652e-12
## [5,] 5.468077e-12 3.667754e-12 3.667754e-12 3.667769e-12 5.466104e-12
## [6,] 5.468077e-12 3.667754e-12 3.667754e-12 3.667769e-12 5.466104e-12
## [7,] 8.232522e-11 8.887102e-11 8.887102e-11 8.887942e-11 8.252371e-11
## [8,] 6.958678e-11 1.113156e-10 1.113156e-10 5.277733e-11 1.113050e-10
## [9,] 2.541708e-10 3.321265e-11 3.068043e-10 9.343661e-11 3.321173e-11
## [10,] 2.751488e-11 3.068043e-10 3.321265e-11 9.343661e-11 3.067958e-10
## [11,] NA NA NA NA NA
## [12,] 1.058271e-07 9.992923e-08 9.992923e-08 1.004762e-07 1.036031e-07
## [13,] 8.869180e-11 7.899621e-11 7.899621e-11 7.900367e-11 8.832704e-11
## [14,] 7.121064e-11 8.006397e-11 8.006397e-11 8.006960e-11 7.077614e-11
## [15,] 4.776556e-12 4.708051e-12 4.708051e-12 4.708080e-12 8.061086e-12
## [16,] 6.318345e-11 6.227727e-11 6.227727e-11 6.227765e-11 1.513084e-11
## [17,] 9.731841e-11 8.315190e-11 8.315190e-11 8.315774e-11 9.764991e-11
## [18,] 1.067306e-07 1.125331e-07 1.125331e-07 1.117199e-07 1.097500e-07
## [19,] 1.087908e-10 7.568434e-11 7.568434e-11 1.419229e-10 7.567712e-11
## [,61] [,62] [,63]
## [1,] 1.455511e-12 1.455516e-12 1.442396e-12
## [2,] 1.455511e-12 1.455516e-12 1.442396e-12
## [3,] 7.376652e-12 7.376679e-12 7.312670e-12
## [4,] 7.376652e-12 7.376679e-12 7.312670e-12
## [5,] 5.466104e-12 5.466127e-12 3.666445e-12
## [6,] 5.466104e-12 5.466127e-12 3.666445e-12
## [7,] 8.252371e-11 8.253150e-11 8.907556e-11
## [8,] 1.113050e-10 5.277230e-11 8.441805e-11
## [9,] 3.067958e-10 9.343348e-11 1.127816e-10
## [10,] 3.321173e-11 9.343348e-11 1.127816e-10
## [11,] NA NA NA
## [12,] 1.036031e-07 1.041702e-07 9.833095e-08
## [13,] 8.832704e-11 8.833538e-11 7.864236e-11
## [14,] 7.077614e-11 7.078111e-11 7.958104e-11
## [15,] 8.061086e-12 8.061134e-12 7.945520e-12
## [16,] 1.513084e-11 1.513094e-11 1.491393e-11
## [17,] 9.764991e-11 9.765678e-11 8.344100e-11
## [18,] 1.097500e-07 1.089570e-07 1.148180e-07
## [19,] 7.567712e-11 1.419093e-10 9.872449e-11
##
## $ML_marginal_prob_each_state_at_branch_top_AT_node
## [,1] [,2] [,3] [,4] [,5]
## [1,] 0.0000000000 1.000000000 0.0000000000 0.0000000000 0.0000000000
## [2,] 0.0000000000 1.000000000 0.0000000000 0.0000000000 0.0000000000
## [3,] 0.0000000000 0.000000000 1.0000000000 0.0000000000 0.0000000000
## [4,] 0.0000000000 1.000000000 0.0000000000 0.0000000000 0.0000000000
## [5,] 0.0000000000 0.000000000 0.0000000000 1.0000000000 0.0000000000
## [6,] 0.0000000000 0.000000000 0.0000000000 1.0000000000 0.0000000000
## [7,] 1.0000000000 0.000000000 0.0000000000 0.0000000000 0.0000000000
## [8,] 0.0000000000 0.000000000 0.0000000000 0.0000000000 1.0000000000
## [9,] 0.0000000000 0.000000000 0.0000000000 0.0000000000 0.0000000000
## [10,] 0.0000000000 0.000000000 0.0000000000 0.0000000000 0.0000000000
## [11,] 0.0160776840 0.016964395 0.0146934722 0.0163026355 0.0158561489
## [12,] 0.1572129082 0.180545403 0.1208833976 0.1631595471 0.1192465370
## [13,] 0.1426694475 0.197812481 0.1177245944 0.1744526778 0.1156043123
## [14,] 0.0023999666 0.957632582 0.0244131585 0.0024545893 0.0023523339
## [15,] 0.0004608755 0.993167686 0.0029940062 0.0004674384 0.0004551525
## [16,] 0.0026796082 0.910352581 0.0412375754 0.0027161239 0.0026477654
## [17,] 0.0005461617 0.000561165 0.0005392326 0.9957180747 0.0005386516
## [18,] 0.0858100839 0.085796605 0.0858311257 0.0858066644 0.2393827954
## [19,] 0.0444147250 0.044412278 0.0444185451 0.0444141041 0.0718827651
## [,6] [,7] [,8] [,9] [,10]
## [1,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.0000000000 1.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 1.0000000000 0.0000000000 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 0.0155250212 0.0155250212 1.652106e-02 1.538556e-02 1.619017e-02
## [12,] 0.1192801962 0.1192801962 1.204967e-03 9.398566e-04 1.127712e-03
## [13,] 0.1156286068 0.1156286068 1.180690e-03 8.790638e-04 1.092712e-03
## [14,] 0.0023523766 0.0023523766 3.976040e-04 9.119640e-05 1.637235e-05
## [15,] 0.0004551576 0.0004551576 2.120132e-04 1.164030e-05 3.149576e-06
## [16,] 0.0026477940 0.0026477940 1.704677e-03 1.505787e-04 1.839828e-05
## [17,] 0.0005386584 0.0005386584 3.734098e-06 3.660410e-06 1.572980e-04
## [18,] 0.1978700841 0.1978700841 5.789539e-04 5.790700e-04 5.789877e-04
## [19,] 0.3609396548 0.3609396548 2.997624e-04 2.997834e-04 2.997685e-04
## [,11] [,12] [,13] [,14] [,15]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
## [11,] 1.602703e-02 1.584515e-02 1.584515e-02 1.582893e-02 0.0166335408
## [12,] 9.326513e-04 9.327824e-04 9.327824e-04 1.016961e-03 0.0011595962
## [13,] 8.711147e-04 8.711964e-04 8.711964e-04 1.064694e-03 0.0013968513
## [14,] 1.602875e-05 1.602889e-05 1.602889e-05 3.313489e-03 0.0004021568
## [15,] 3.108288e-06 3.108305e-06 3.108305e-06 3.670626e-04 0.0002124149
## [16,] 1.816858e-05 1.816868e-05 1.816868e-05 2.503933e-02 0.0017056937
## [17,] 3.658458e-06 3.658481e-06 3.658481e-06 3.710818e-06 0.0001594653
## [18,] 1.097067e-03 9.570282e-04 9.570282e-04 5.790247e-04 0.0005789424
## [19,] 3.920884e-04 1.367966e-03 1.367966e-03 2.997752e-04 0.0002997603
## [,16] [,17] [,18] [,19] [,20]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 1.650737e-02 1.631545e-02 1.631545e-02 1.549804e-02 1.527719e-02
## [12,] 1.011333e-03 1.011475e-03 1.011475e-03 9.583023e-04 8.101429e-04
## [13,] 1.057434e-03 1.057545e-03 1.057545e-03 9.893510e-04 7.872959e-04
## [14,] 3.936338e-04 3.936374e-04 3.936374e-04 9.224065e-05 9.028579e-05
## [15,] 2.116629e-04 2.116632e-04 2.116632e-04 1.166235e-05 1.162107e-05
## [16,] 1.703790e-03 1.703791e-03 1.703791e-03 1.515956e-04 1.496920e-04
## [17,] 3.708866e-06 3.708889e-06 3.708889e-06 1.562971e-04 3.635178e-06
## [18,] 1.096981e-03 9.569533e-04 9.569533e-04 5.790585e-04 1.097201e-03
## [19,] 3.920802e-04 1.367929e-03 1.367929e-03 2.997813e-04 3.921012e-04
## [,21] [,22] [,23] [,24] [,25]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 1.511097e-02 1.511097e-02 1.614889e-02 1.596446e-02 1.596446e-02
## [12,] 8.102567e-04 8.102567e-04 9.527048e-04 9.528387e-04 9.528387e-04
## [13,] 7.873782e-04 7.873782e-04 9.786408e-04 9.787432e-04 9.787432e-04
## [14,] 9.028660e-05 9.028660e-05 1.621229e-05 1.621244e-05 1.621244e-05
## [15,] 1.162108e-05 1.162108e-05 3.130343e-06 3.130360e-06 3.130360e-06
## [16,] 1.496928e-04 1.496928e-04 1.829128e-05 1.829138e-05 1.829138e-05
## [17,] 3.635201e-06 3.635201e-06 1.562132e-04 1.562142e-04 1.562142e-04
## [18,] 9.571451e-04 9.571451e-04 1.097046e-03 9.570092e-04 9.570092e-04
## [19,] 1.368025e-03 1.368025e-03 3.920863e-04 1.367957e-03 1.367957e-03
## [,26] [,27] [,28] [,29] [,30]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 1.569058e-02 1.569058e-02 1.552501e-02 1.591181e-02 1.644725e-02
## [12,] 8.047376e-04 8.047376e-04 8.048507e-04 1.422014e-05 1.570380e-05
## [13,] 7.802268e-04 7.802268e-04 7.803085e-04 1.410807e-05 1.664090e-05
## [14,] 1.586884e-05 1.586884e-05 1.586898e-05 1.717255e-05 3.707385e-06
## [15,] 3.089073e-06 3.089073e-06 3.089090e-06 2.454229e-06 1.490495e-06
## [16,] 1.806168e-05 1.806168e-05 1.806177e-05 8.922938e-05 1.140508e-05
## [17,] 3.633249e-06 3.633249e-06 3.633271e-06 5.106868e-08 1.462425e-06
## [18,] 2.151483e-03 2.151483e-03 1.335153e-03 7.823014e-06 7.822268e-06
## [19,] 1.789228e-03 1.789228e-03 1.004892e-02 4.057897e-06 4.057762e-06
## [,31] [,32] [,33] [,34] [,35]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 1.635090e-02 1.622655e-02 1.622655e-02 1.569161e-02 1.556382e-02
## [12,] 1.416212e-05 1.416346e-05 1.416346e-05 1.360999e-05 1.206903e-05
## [13,] 1.403836e-05 1.403928e-05 1.403928e-05 1.336199e-05 1.142308e-05
## [14,] 3.654566e-06 3.654588e-06 3.654588e-06 9.114018e-07 8.984172e-07
## [15,] 1.485808e-06 1.485810e-06 1.485810e-06 1.201652e-07 1.197873e-07
## [16,] 1.139284e-05 1.139284e-05 1.139284e-05 1.415887e-06 1.403650e-06
## [17,] 5.105059e-08 5.105080e-08 5.105080e-08 1.442858e-06 5.036753e-08
## [18,] 1.247748e-05 1.121842e-05 1.121842e-05 7.823321e-06 1.247916e-05
## [19,] 4.898106e-06 1.366139e-05 1.366139e-05 4.057953e-06 4.898298e-06
## [,36] [,37] [,38] [,39] [,40]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 1.544800e-02 1.544800e-02 1.612154e-02 1.599968e-02 1.599968e-02
## [12,] 1.207017e-05 1.207017e-05 1.355218e-05 1.355346e-05 1.355346e-05
## [13,] 1.142382e-05 1.142382e-05 1.327565e-05 1.327652e-05 1.327652e-05
## [14,] 8.984227e-07 8.984227e-07 2.219962e-07 2.219975e-07 2.219975e-07
## [15,] 1.197875e-07 1.197875e-07 4.209013e-08 4.209029e-08 4.209029e-08
## [16,] 1.403655e-06 1.403655e-06 2.428177e-07 2.428186e-07 2.428186e-07
## [17,] 5.036774e-08 5.036774e-08 1.442340e-06 1.442346e-06 1.442346e-06
## [18,] 1.121993e-05 1.121993e-05 1.247797e-05 1.121886e-05 1.121886e-05
## [19,] 1.366204e-05 1.366204e-05 4.898162e-06 1.366158e-05 1.366158e-05
## [,41] [,42] [,43] [,44] [,45]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 1.585428e-02 1.585428e-02 1.573867e-02 1.598666e-02 1.587115e-02
## [12,] 1.201291e-05 1.201291e-05 1.201405e-05 1.409964e-05 1.276836e-05
## [13,] 1.135477e-05 1.135477e-05 1.135552e-05 1.551313e-05 1.308318e-05
## [14,] 2.188347e-07 2.188347e-07 2.188360e-07 1.730512e-05 1.705694e-05
## [15,] 4.171247e-08 4.171247e-08 4.171263e-08 2.456732e-06 2.452046e-06
## [16,] 2.407201e-07 2.407201e-07 2.407210e-07 8.928058e-05 8.918474e-05
## [17,] 5.034965e-08 5.034965e-08 5.034986e-08 1.456243e-06 5.083479e-08
## [18,] 1.890566e-05 1.890566e-05 1.461582e-05 7.822910e-06 1.247850e-05
## [19,] 1.649070e-05 1.649070e-05 5.735893e-05 4.057878e-06 4.898223e-06
## [,46] [,47] [,48] [,49] [,50]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 1.575200e-02 1.575200e-02 1.642887e-02 1.630367e-02 1.630367e-02
## [12,] 1.276957e-05 1.276957e-05 1.404892e-05 1.405024e-05 1.405024e-05
## [13,] 1.308410e-05 1.308410e-05 1.543201e-05 1.543310e-05 1.543310e-05
## [14,] 1.705704e-05 1.705704e-05 3.682781e-06 3.682803e-06 3.682803e-06
## [15,] 2.452048e-06 2.452048e-06 1.488312e-06 1.488314e-06 1.488314e-06
## [16,] 8.918478e-05 8.918478e-05 1.139938e-05 1.139938e-05 1.139938e-05
## [17,] 5.083500e-08 5.083500e-08 1.455725e-06 1.455731e-06 1.455731e-06
## [18,] 1.121934e-05 1.121934e-05 1.247731e-05 1.121827e-05 1.121827e-05
## [19,] 1.366179e-05 1.366179e-05 4.898087e-06 1.366133e-05 1.366133e-05
## [,51] [,52] [,53] [,54] [,55]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 1.617055e-02 1.617055e-02 1.605161e-02 1.564179e-02 1.552512e-02
## [12,] 1.271931e-05 1.271931e-05 1.272051e-05 1.224174e-05 1.224289e-05
## [13,] 1.301921e-05 1.301921e-05 1.302013e-05 1.239130e-05 1.239217e-05
## [14,] 3.629984e-06 3.629984e-06 3.630006e-06 9.053533e-07 9.053588e-07
## [15,] 1.483627e-06 1.483627e-06 1.483629e-06 1.199892e-07 1.199893e-07
## [16,] 1.138715e-05 1.138715e-05 1.138715e-05 1.410187e-06 1.410192e-06
## [17,] 5.081691e-08 5.081691e-08 5.081712e-08 1.436158e-06 1.436164e-06
## [18,] 1.890467e-05 1.890467e-05 1.461505e-05 1.247899e-05 1.121978e-05
## [19,] 1.649045e-05 1.649045e-05 5.735787e-05 4.898279e-06 1.366198e-05
## [,56] [,57] [,58] [,59] [,60]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 1.552512e-02 1.536056e-02 1.536056e-02 1.525015e-02 1.593451e-02
## [12,] 1.224289e-05 1.091259e-05 1.091259e-05 1.091362e-05 1.219282e-05
## [13,] 1.239217e-05 1.059379e-05 1.059379e-05 1.059454e-05 1.231187e-05
## [14,] 9.053588e-07 8.923742e-07 8.923742e-07 8.923796e-07 2.205242e-07
## [15,] 1.199893e-07 1.196115e-07 1.196115e-07 1.196117e-07 4.191429e-08
## [16,] 1.410192e-06 1.397955e-06 1.397955e-06 1.397961e-06 2.418411e-07
## [17,] 1.436164e-06 5.013385e-08 5.013385e-08 5.013406e-08 1.435646e-06
## [18,] 1.121978e-05 1.890721e-05 1.890721e-05 1.461702e-05 1.890541e-05
## [19,] 1.366198e-05 1.649109e-05 1.649109e-05 5.736058e-05 1.649064e-05
## [,61] [,62] [,63]
## [1,] 0.000000e+00 0.000000e+00 0.000000e+00
## [2,] 0.000000e+00 0.000000e+00 0.000000e+00
## [3,] 0.000000e+00 0.000000e+00 0.000000e+00
## [4,] 0.000000e+00 0.000000e+00 0.000000e+00
## [5,] 0.000000e+00 0.000000e+00 0.000000e+00
## [6,] 0.000000e+00 0.000000e+00 0.000000e+00
## [7,] 0.000000e+00 0.000000e+00 0.000000e+00
## [8,] 0.000000e+00 0.000000e+00 0.000000e+00
## [9,] 0.000000e+00 0.000000e+00 0.000000e+00
## [10,] 0.000000e+00 0.000000e+00 0.000000e+00
## [11,] 1.593451e-02 1.581806e-02 1.563589e-02
## [12,] 1.219282e-05 1.219397e-05 1.086402e-05
## [13,] 1.231187e-05 1.231274e-05 1.053030e-05
## [14,] 2.205242e-07 2.205255e-07 2.173627e-07
## [15,] 4.191429e-08 4.191445e-08 4.153664e-08
## [16,] 2.418411e-07 2.418420e-07 2.397435e-07
## [17,] 1.435646e-06 1.435652e-06 5.011597e-08
## [18,] 1.890541e-05 1.461562e-05 2.533428e-05
## [19,] 1.649064e-05 5.735866e-05 6.923645e-05
##
## $relative_probs_of_each_state_at_bottom_of_root_branch
## [1] 0.01607768 0.01696440 0.01469347 0.01630264 0.01585615 0.01552502
## [7] 0.01552502 0.01652106 0.01538556 0.01619017 0.01602703 0.01584515
## [13] 0.01584515 0.01582893 0.01663354 0.01650737 0.01631545 0.01631545
## [19] 0.01549804 0.01527719 0.01511097 0.01511097 0.01614889 0.01596446
## [25] 0.01596446 0.01569058 0.01569058 0.01552501 0.01591181 0.01644725
## [31] 0.01635090 0.01622655 0.01622655 0.01569161 0.01556382 0.01544800
## [37] 0.01544800 0.01612154 0.01599968 0.01599968 0.01585428 0.01585428
## [43] 0.01573867 0.01598666 0.01587115 0.01575200 0.01575200 0.01642887
## [49] 0.01630367 0.01630367 0.01617055 0.01617055 0.01605161 0.01564179
## [55] 0.01552512 0.01552512 0.01536056 0.01536056 0.01525015 0.01593451
## [61] 0.01593451 0.01581806 0.01563589
##
## $total_loglikelihood
## [1] -12.50069
##
## $inputs
## $inputs$geogfn
## [1] "~/Dropbox (AMNH)/Research/Petaluridae_phylogeny/Divergence_dating/condensed_biogeography.txt"
##
## $inputs$trfn
## [1] "~/Desktop/Jessica_calibrated_two/Jessica_calibrated_one/biogeobears.tre"
##
## $inputs$abbr
## [1] "default"
##
## $inputs$description
## [1] "defaults"
##
## $inputs$BioGeoBEARS_model_object
## An object of class "BioGeoBEARS_model"
## Slot "params_table":
## type init min max est note
## d free 0.007455278 1.0e-12 5.00000 0.007455278 works
## e free 1.104879565 1.0e-12 5.00000 1.104879565 works
## a fixed 0.000000000 1.0e-12 5.00000 0.000000000 works
## b free 1.000000000 1.0e-12 1.00000 1.000000000 non-stratified only
## x fixed 0.000000000 -2.5e+00 2.50000 0.000000000 works
## n fixed 0.000000000 -1.0e+01 10.00000 0.000000000 works
## w fixed 1.000000000 -1.0e+01 10.00000 1.000000000 works
## u fixed 0.000000000 -1.0e+01 10.00000 0.000000000 works
## j free 0.000010000 1.0e-05 1.99999 0.000010000 works
## ysv 2-j 2.999990000 1.0e-05 3.00000 1.999990000 works
## ys ysv*1/2 1.999990000 1.0e-05 2.00000 0.999995000 works
## y ysv*1/2 1.000000000 1.0e-05 1.00000 0.999995000 works
## s fixed 0.000000100 1.0e-05 1.00000 0.000000100 works
## v ysv*1/2 1.000000000 1.0e-05 1.00000 0.999995000 works
## mx01 fixed 0.000100000 1.0e-04 0.99990 0.000100000 works
## mx01j mx01 0.000100000 1.0e-04 0.99990 0.000100000 works
## mx01y mx01 0.000100000 1.0e-04 0.99990 0.000100000 works
## mx01s mx01 0.000100000 1.0e-04 0.99990 0.000100000 works
## mx01v fixed 0.500000000 1.0e-04 0.99990 0.500000000 works
## mx01r fixed 0.500000000 1.0e-04 0.99990 0.500000000 no
## mf fixed 0.100000000 5.0e-03 0.99500 0.100000000 yes
## dp fixed 1.000000000 5.0e-03 0.99500 1.000000000 yes
## fdp fixed 0.000000000 5.0e-03 0.99500 0.000000000 yes
## desc
## d anagenesis: rate of 'dispersal' (range expansion)
## e anagenesis: rate of 'extinction' (range contraction)
## a anagenesis: rate of range-switching (i.e. for a standard char.)
## b anagenesis: exponent on branch lengths
## x exponent on distance (modifies d, j, a)
## n exponent on environmental distance (modifies d, j, a)
## w exponent on manual dispersal multipliers (modifies d, j, a)
## u anagenesis: exponent on extinction risk with area (modifies e)
## j cladogenesis: relative per-event weight of jump dispersal
## ysv cladogenesis: y+s+v
## ys cladogenesis: y+s
## y cladogenesis: relative per-event weight of sympatry (range-copying)
## s cladogenesis: relative per-event weight of subset speciation
## v cladogenesis: relative per-event weight of vicariant speciation
## mx01 cladogenesis: controls range size of smaller daughter
## mx01j cladogenesis: controls range size of smaller daughter
## mx01y cladogenesis: controls range size of smaller daughter
## mx01s cladogenesis: controls range size of smaller daughter
## mx01v cladogenesis: controls range size of smaller daughter
## mx01r root: controls range size probabilities of root
## mf mean frequency of truly sampling OTU of interest
## dp detection probability per true sample of OTU of interest
## fdp false detection of OTU probability per true taphonomic control sample
##
##
## $inputs$timesfn
## [1] NA
##
## $inputs$distsfn
## [1] NA
##
## $inputs$dispersal_multipliers_fn
## [1] NA
##
## $inputs$area_of_areas_fn
## [1] NA
##
## $inputs$areas_allowed_fn
## [1] NA
##
## $inputs$areas_adjacency_fn
## [1] NA
##
## $inputs$detects_fn
## [1] NA
##
## $inputs$controls_fn
## [1] NA
##
## $inputs$max_range_size
## [1] 3
##
## $inputs$force_sparse
## [1] FALSE
##
## $inputs$use_detection_model
## [1] FALSE
##
## $inputs$print_optim
## [1] TRUE
##
## $inputs$printlevel
## [1] 0
##
## $inputs$on_NaN_error
## [1] -1e+50
##
## $inputs$wd
## [1] "/Users/ethantolman/Dropbox (AMNH)/Research/Petaluridae_phylogeny/revbayes"
##
## $inputs$num_cores_to_use
## [1] 6
##
## $inputs$cluster_already_open
## [1] FALSE
##
## $inputs$use_optimx
## [1] TRUE
##
## $inputs$rescale_params
## [1] FALSE
##
## $inputs$return_condlikes_table
## [1] TRUE
##
## $inputs$calc_TTL_loglike_from_condlikes_table
## [1] TRUE
##
## $inputs$calc_ancprobs
## [1] TRUE
##
## $inputs$speedup
## [1] TRUE
##
## $inputs$include_null_range
## [1] FALSE
##
## $inputs$useAmbiguities
## [1] FALSE
##
## $inputs$min_branchlength
## [1] 1e-06
##
## $inputs$allow_null_tips
## [1] FALSE
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[1]]
## [1] 0
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[2]]
## [1] 1
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[3]]
## [1] 2
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[4]]
## [1] 3
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[5]]
## [1] 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[6]]
## [1] 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[7]]
## [1] 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[8]]
## [1] 0 1
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[9]]
## [1] 0 2
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[10]]
## [1] 0 3
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[11]]
## [1] 0 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[12]]
## [1] 0 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[13]]
## [1] 0 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[14]]
## [1] 1 2
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[15]]
## [1] 1 3
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[16]]
## [1] 1 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[17]]
## [1] 1 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[18]]
## [1] 1 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[19]]
## [1] 2 3
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[20]]
## [1] 2 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[21]]
## [1] 2 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[22]]
## [1] 2 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[23]]
## [1] 3 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[24]]
## [1] 3 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[25]]
## [1] 3 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[26]]
## [1] 4 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[27]]
## [1] 4 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[28]]
## [1] 5 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[29]]
## [1] 0 1 2
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[30]]
## [1] 0 1 3
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[31]]
## [1] 0 1 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[32]]
## [1] 0 1 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[33]]
## [1] 0 1 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[34]]
## [1] 0 2 3
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[35]]
## [1] 0 2 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[36]]
## [1] 0 2 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[37]]
## [1] 0 2 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[38]]
## [1] 0 3 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[39]]
## [1] 0 3 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[40]]
## [1] 0 3 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[41]]
## [1] 0 4 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[42]]
## [1] 0 4 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[43]]
## [1] 0 5 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[44]]
## [1] 1 2 3
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[45]]
## [1] 1 2 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[46]]
## [1] 1 2 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[47]]
## [1] 1 2 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[48]]
## [1] 1 3 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[49]]
## [1] 1 3 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[50]]
## [1] 1 3 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[51]]
## [1] 1 4 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[52]]
## [1] 1 4 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[53]]
## [1] 1 5 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[54]]
## [1] 2 3 4
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[55]]
## [1] 2 3 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[56]]
## [1] 2 3 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[57]]
## [1] 2 4 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[58]]
## [1] 2 4 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[59]]
## [1] 2 5 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[60]]
## [1] 3 4 5
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[61]]
## [1] 3 4 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[62]]
## [1] 3 5 6
##
## $inputs$all_geog_states_list_usually_inferred_from_areas_maxareas[[63]]
## [1] 4 5 6
##
##
##
## $outputs
## An object of class "BioGeoBEARS_model"
## Slot "params_table":
## type init min max est note
## d free 0.007455278 1.0e-12 5.00000 0.007455278 works
## e free 1.104879565 1.0e-12 5.00000 1.104879565 works
## a fixed 0.000000000 1.0e-12 5.00000 0.000000000 works
## b free 1.000000000 1.0e-12 1.00000 1.000000000 non-stratified only
## x fixed 0.000000000 -2.5e+00 2.50000 0.000000000 works
## n fixed 0.000000000 -1.0e+01 10.00000 0.000000000 works
## w fixed 1.000000000 -1.0e+01 10.00000 1.000000000 works
## u fixed 0.000000000 -1.0e+01 10.00000 0.000000000 works
## j free 0.000010000 1.0e-05 1.99999 0.000010000 works
## ysv 2-j 2.999990000 1.0e-05 3.00000 1.999990000 works
## ys ysv*1/2 1.999990000 1.0e-05 2.00000 0.999995000 works
## y ysv*1/2 1.000000000 1.0e-05 1.00000 0.999995000 works
## s fixed 0.000000100 1.0e-05 1.00000 0.000000100 works
## v ysv*1/2 1.000000000 1.0e-05 1.00000 0.999995000 works
## mx01 fixed 0.000100000 1.0e-04 0.99990 0.000100000 works
## mx01j mx01 0.000100000 1.0e-04 0.99990 0.000100000 works
## mx01y mx01 0.000100000 1.0e-04 0.99990 0.000100000 works
## mx01s mx01 0.000100000 1.0e-04 0.99990 0.000100000 works
## mx01v fixed 0.500000000 1.0e-04 0.99990 0.500000000 works
## mx01r fixed 0.500000000 1.0e-04 0.99990 0.500000000 no
## mf fixed 0.100000000 5.0e-03 0.99500 0.100000000 yes
## dp fixed 1.000000000 5.0e-03 0.99500 1.000000000 yes
## fdp fixed 0.000000000 5.0e-03 0.99500 0.000000000 yes
## desc
## d anagenesis: rate of 'dispersal' (range expansion)
## e anagenesis: rate of 'extinction' (range contraction)
## a anagenesis: rate of range-switching (i.e. for a standard char.)
## b anagenesis: exponent on branch lengths
## x exponent on distance (modifies d, j, a)
## n exponent on environmental distance (modifies d, j, a)
## w exponent on manual dispersal multipliers (modifies d, j, a)
## u anagenesis: exponent on extinction risk with area (modifies e)
## j cladogenesis: relative per-event weight of jump dispersal
## ysv cladogenesis: y+s+v
## ys cladogenesis: y+s
## y cladogenesis: relative per-event weight of sympatry (range-copying)
## s cladogenesis: relative per-event weight of subset speciation
## v cladogenesis: relative per-event weight of vicariant speciation
## mx01 cladogenesis: controls range size of smaller daughter
## mx01j cladogenesis: controls range size of smaller daughter
## mx01y cladogenesis: controls range size of smaller daughter
## mx01s cladogenesis: controls range size of smaller daughter
## mx01v cladogenesis: controls range size of smaller daughter
## mx01r root: controls range size probabilities of root
## mf mean frequency of truly sampling OTU of interest
## dp detection probability per true sample of OTU of interest
## fdp false detection of OTU probability per true taphonomic control sample
##
##
## $optim_result
## p1 p2 p3 p4 value fevals gevals niter convcode
## bobyqa 0.007455278 1.10488 1 1e-05 -12.50069 162 NA NA 0
## kkt1 kkt2 xtime
## bobyqa FALSE TRUE 3.122
##
## attr(,"class")
## [1] "calc_loglike_sp_results"scriptdir = np(system.file("extdata/a_scripts", package="BioGeoBEARS"))
plot_BioGeoBEARS_results(results_object, plotwhat = "text")## LnL nparams d e b j
## 1 -12.50069 4 0.007455278 1.10488 1 1e-05plot_BioGeoBEARS_results(results_object, plotwhat = "pie", plotlegend = T, plotsplits = F)## LnL nparams d e b j
## 1 -12.50069 4 0.007455278 1.10488 1 1e-05dev.off() # Turn off PDF## pdf
## 3cmdstr = paste("open ", pdffn, sep="")
system(cmdstr) # Plot it# Set up BAYAREALIKE model
# No subset sympatry
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","init"] = 0.0
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","est"] = 0.0
# No vicariance
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","init"] = 0.0
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","est"] = 0.0
# No jump dispersal/founder-event speciation
# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = 0.01
# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = 0.01
# Adjust linkage between parameters
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ysv","type"] = "1-j"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ys","type"] = "ysv*1/1"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["y","type"] = "1-j"
# Only sympatric/range-copying (y) events allowed, and with
# exact copying (both descendants always the same size as the ancestor)
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","init"] = 0.9999
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","est"] = 0.9999
# Check the inputs; fixing any initial ("init") values outside min/max
BioGeoBEARS_run_object = fix_BioGeoBEARS_params_minmax(BioGeoBEARS_run_object=BioGeoBEARS_run_object)
check_BioGeoBEARS_run(BioGeoBEARS_run_object)## [1] TRUErunslow = TRUE
resfn = "Petaluridae_BAYAREALIKE_M0_unconstrained_v1.Rdata"
if (runslow)
{
res = bears_optim_run(BioGeoBEARS_run_object)
res
save(res, file=resfn)
resBAYAREALIKE = res
} else {
# Loads to "res"
load(resfn)
resBAYAREALIKE = res
}## [1] "Note: tipranges_to_tip_condlikes_of_data_on_each_state() is converting a states_list with (0-based) numbers to the equivalent areanames"
##
## Your computer has 8 cores.
##
## Your computer has 8 cores. You have chosen to use:
## num_cores_to_use = 6 cores for the matrix exponentiations in the likelihood calculations.
## Started cluster with 6 cores.
##
## [1] "parscale:"
## [1] 5.00000 5.00000 1.00000 1.99998
##
##
## NOTE: Before running optimx(), here is a test calculation of the data likelihood
## using calc_loglike_for_optim() on initial parameter values, with printlevel=2...
## if this crashes, the error messages are more helpful
## than those from inside optimx().
##
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.698 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.614
##
## calc_loglike_for_optim() on initial parameters loglike=-12.61403
##
##
##
## Calculation of likelihood on initial parameters: successful.
##
## Now starting Maximum Likelihood (ML) parameter optimization with optimx()...
##
##
##
## Printing any warnings() that occurred during calc_loglike_for_optim():
##
## NULL
##
##
## Results of optimx_scalecheck() below. Note: sometimes rescaling parameters may be helpful for ML searches, when the parameters have much different absolute sizes. This can be attempted by setting BioGeoBEARS_run_object$rescale_params = TRUE.
##
## $lpratio
## [1] 4
##
## $lbratio
## [1] 0.69897
##
## Maximizing -- use negfn and neggr
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.698 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.614## Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower, : Parameters or bounds appear to have different scalings.
## This can cause poor performance in optimization.
## It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.## Warning in (function (npt = min(n + 2L, 2L * n), rhobeg = NA, rhoend = NA, :
## unused control arguments ignored## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.698 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.614
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.2 0.698 0 1 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -25.181
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.4 0.698 0 1 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -33.246
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.2 0.898 0 1 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -23.039
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.2 0.698 0 0.8 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -25.177
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.2 0.698 0 1 0 0 1 0 0.4 0.6 0.6 0.6 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -25.181
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0 0.698 0 1 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -14.586
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0 0.898 0 1 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -14.586
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0 1.025 0 1 0 0 1 0 0.354 0.646 0.646 0.646 0 0 0 0 1 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -15.369
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0 0.901 0 1 0 0 1 0 0.1 0.9 0.9 0.9 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -14.64
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0 0.898 0 0.965 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -14.576
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.852 0 0.952 0 0 1 0 0.215 0.785 0.785 0.785 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.644
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.91 0 0.968 0 0 1 0 0.215 0.785 0.785 0.785 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.637
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.899 0 0.96 0 0 1 0 0.181 0.819 0.819 0.819 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.527
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.908 0 0.931 0 0 1 0 0.155 0.845 0.845 0.845 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.482
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.93 0 0.858 0 0 1 0 0.129 0.871 0.871 0.871 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.497
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.022 0.908 0 0.931 0 0 1 0 0.155 0.845 0.845 0.845 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -15.425
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.914 0 0.911 0 0 1 0 0.143 0.857 0.857 0.857 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.479
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.922 0 0.917 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.478
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.919 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.478
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 0.919 0 0.919 0 0 1 0 0.143 0.857 0.857 0.857 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.479
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 0.919 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.136
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.919 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.117
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.918 0 0.917 0 0 1 0 0.146 0.854 0.854 0.854 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.115
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.917 0 0.916 0 0 1 0 0.147 0.853 0.853 0.853 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.126
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.917 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.111
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.918 0 0.916 0 0 1 0 0.146 0.854 0.854 0.854 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.112
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.917 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.105
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.917 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.102
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.917 0 0 1 0 0.144 0.856 0.856 0.856 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.098
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.917 0 0.917 0 0 1 0 0.143 0.857 0.857 0.857 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.094
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.917 0 0.918 0 0 1 0 0.143 0.857 0.857 0.857 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.087
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.917 0 0.919 0 0 1 0 0.141 0.859 0.859 0.859 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.081
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.006 0.917 0 0.919 0 0 1 0 0.14 0.86 0.86 0.86 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.141
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.917 0 0.918 0 0 1 0 0.141 0.859 0.859 0.859 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.076
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.003 0.917 0 0.919 0 0 1 0 0.14 0.86 0.86 0.86 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.066
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.918 0 0 1 0 0.141 0.859 0.859 0.859 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.081
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.003 0.917 0 0.918 0 0 1 0 0.14 0.86 0.86 0.86 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.066
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.003 0.917 0 0.919 0 0 1 0 0.14 0.86 0.86 0.86 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.063
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.919 0 0 1 0 0.139 0.861 0.861 0.861 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.06
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.919 0 0 1 0 0.139 0.861 0.861 0.861 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.06
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.919 0 0 1 0 0.139 0.861 0.861 0.861 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.058
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.919 0 0 1 0 0.139 0.861 0.861 0.861 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.057
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.919 0 0 1 0 0.139 0.861 0.861 0.861 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.055
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.919 0 0 1 0 0.139 0.861 0.861 0.861 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.054
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.919 0 0 1 0 0.139 0.861 0.861 0.861 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.054
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.919 0 0 1 0 0.139 0.861 0.861 0.861 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.054
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.919 0 0 1 0 0.139 0.861 0.861 0.861 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.053
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.919 0 0 1 0 0.138 0.862 0.862 0.862 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.05
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.003 0.917 0 0.92 0 0 1 0 0.138 0.862 0.862 0.862 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.045
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.004 0.917 0 0.92 0 0 1 0 0.136 0.864 0.864 0.864 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.035
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.917 0 0.922 0 0 1 0 0.133 0.867 0.867 0.867 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.02
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.917 0 0.924 0 0 1 0 0.128 0.872 0.872 0.872 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.006
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.916 0 0.925 0 0 1 0 0.126 0.874 0.874 0.874 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.004
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.916 0 0.925 0 0 1 0 0.126 0.874 0.874 0.874 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.004
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.916 0 0.925 0 0 1 0 0.126 0.874 0.874 0.874 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.008
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.916 0 0.925 0 0 1 0 0.126 0.874 0.874 0.874 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.002
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.917 0 0.925 0 0 1 0 0.126 0.874 0.874 0.874 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.99
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.917 0 0.925 0 0 1 0 0.126 0.874 0.874 0.874 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.959
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.925 0 0 1 0 0.126 0.874 0.874 0.874 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.955
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 0.917 0 0.925 0 0 1 0 0.126 0.874 0.874 0.874 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.948
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.917 0 0.925 0 0 1 0 0.124 0.876 0.876 0.876 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.936
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.917 0 0.927 0 0 1 0 0.121 0.879 0.879 0.879 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.915
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.917 0 0.928 0 0 1 0 0.118 0.882 0.882 0.882 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.905
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.005 0.917 0 0.93 0 0 1 0 0.116 0.884 0.884 0.884 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.894
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.916 0 0.931 0 0 1 0 0.113 0.887 0.887 0.887 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.884
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 0.916 0 0.934 0 0 1 0 0.108 0.892 0.892 0.892 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.866
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 0.916 0 0.936 0 0 1 0 0.104 0.896 0.896 0.896 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.877
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 0.917 0 0.935 0 0 1 0 0.109 0.891 0.891 0.891 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.902
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.916 0 0.934 0 0 1 0 0.108 0.892 0.892 0.892 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.808
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.916 0 0.935 0 0 1 0 0.109 0.891 0.891 0.891 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.797
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.916 0 0.935 0 0 1 0 0.108 0.892 0.892 0.892 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.794
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.915 0 0.936 0 0 1 0 0.108 0.892 0.892 0.892 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.794
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.915 0 0.936 0 0 1 0 0.109 0.891 0.891 0.891 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.797
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.915 0 0.936 0 0 1 0 0.108 0.892 0.892 0.892 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.79
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.915 0 0.936 0 0 1 0 0.107 0.893 0.893 0.893 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.782
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.915 0 0.937 0 0 1 0 0.105 0.895 0.895 0.895 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.769
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 0.914 0 0.938 0 0 1 0 0.104 0.896 0.896 0.896 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.758
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.004 0.914 0 0.94 0 0 1 0 0.102 0.898 0.898 0.898 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.738
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 0.913 0 0.943 0 0 1 0 0.097 0.903 0.903 0.903 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.696
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.005 0.91 0 0.95 0 0 1 0 0.088 0.912 0.912 0.912 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.61
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.006 0.906 0 0.963 0 0 1 0 0.069 0.931 0.931 0.931 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.443
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 0.896 0 0.991 0 0 1 0 0.031 0.969 0.969 0.969 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.056
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.009 0.893 0 1 0 0 1 0 0.016 0.984 0.984 0.984 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.866
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.009 0.894 0 1 0 0 1 0 0.015 0.985 0.985 0.985 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.831
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 0.896 0 1 0 0 1 0 0.015 0.985 0.985 0.985 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.775
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 0.896 0 1 0 0 1 0 0.015 0.985 0.985 0.985 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.777
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 0.896 0 1 0 0 1 0 0.015 0.985 0.985 0.985 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.763
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 0.895 0 1 0 0 1 0 0.015 0.985 0.985 0.985 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.755
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.006 0.895 0 1 0 0 1 0 0.014 0.986 0.986 0.986 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.748
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.006 0.895 0 1 0 0 1 0 0.014 0.986 0.986 0.986 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.744
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.006 0.895 0 1 0 0 1 0 0.013 0.987 0.987 0.987 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.733
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 0.895 0 1 0 0 1 0 0.012 0.988 0.988 0.988 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.712
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.007 0.895 0 1 0 0 1 0 0.01 0.99 0.99 0.99 0 0 0 0 1 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -12.694
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.007 0.895 0 1 0 0 1 0 0.01 0.99 0.99 0.99 0 0 0 0 1 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -12.686
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 0.895 0 1 0 0 1 0 0.008 0.992 0.992 0.992 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.667
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 0.895 0 1 0 0 1 0 0.006 0.994 0.994 0.994 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.63
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.552
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.548
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 0.896 0 0.999 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.548
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.548
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.554
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.544
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.895 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.544
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.553
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.556
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.544
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.545
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.542
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.542
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.985 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.519
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.806 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.569
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.941 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.529
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.851 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.554
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.918 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.535
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.873 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.547
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.907 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.538
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.885 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.544
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 1.1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.474
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.9 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.848
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 1.05 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.483
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.95 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.659
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 1.025 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.505
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.975 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.592
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 1.012 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.521
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.987 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.565
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.543
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.539
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.542
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.54
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.985 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.528
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.806 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.581
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.941 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.532
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.851 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.557
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.918 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.536
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.873 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.548
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.907 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.538
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.885 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.544
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 0.896 0 1.1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.547
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.9 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.949
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 0.896 0 1.05 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.502
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.95 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.682
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 0.896 0 1.025 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.51
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.975 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.598
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.008 0.896 0 1.012 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.523
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.987 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.566
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.985 0 1.1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.452
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.806 0 0.9 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.876
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.941 0 1.05 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.471
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.851 0 0.95 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.672
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.918 0 1.025 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.499
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.873 0 0.975 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.598
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.907 0 1.012 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.518
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.885 0 0.987 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.568
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.555
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.554
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.545
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.544
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.542
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.542
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.008 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.985 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.52
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.806 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.567
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.941 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.53
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.851 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.553
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.918 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.535
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.873 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.547
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.907 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.538
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.885 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.544
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 1.1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.476
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.9 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.847
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 1.05 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.483
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.95 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.658
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 1.025 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.505
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.975 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.592
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 1.012 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.521
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.007 0.896 0 0.987 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.564
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.543
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.539
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.542
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.54
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.541
##
##
## This is the output from optim, optimx, or GenSA. Check the help on those functions to
## interpret this output and check for convergence issues:
##
## p1 p2 p3 p4 value fevals gevals niter convcode
## bobyqa 0.007421225 0.8957392 1 1e-05 -12.54107 128 NA NA 0
## kkt1 kkt2 xtime
## bobyqa FALSE TRUE 2.599
##
##
## Stopping cluster with 6 cores.# Set up BAYAREALIKE+J model
# Get the ML parameter values from the 2-parameter nested model
# (this will ensure that the 3-parameter model always does at least as good)
dstart = resBAYAREALIKE$outputs@params_table["d","est"]
estart = resBAYAREALIKE$outputs@params_table["e","est"]
jstart = 0.0001
# Input starting values for d, e
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","init"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","est"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","init"] = estart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","est"] = estart
# No subset sympatry
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","init"] = 0.0
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","est"] = 0.0
# No vicariance
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","init"] = 0.0
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","est"] = 0.0
# *DO* allow jump dispersal/founder-event speciation (set the starting value close to 0)
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = jstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = jstart
# Under BAYAREALIKE+J, the max of "j" should be 1, not 3 (as is default in DEC+J) or 2 (as in DIVALIKE+J)
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","max"] = 0.99999
# Adjust linkage between parameters
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ysv","type"] = "1-j"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ys","type"] = "ysv*1/1"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["y","type"] = "1-j"
# Only sympatric/range-copying (y) events allowed, and with
# exact copying (both descendants always the same size as the ancestor)
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","init"] = 0.9999
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","est"] = 0.9999
# NOTE (NJM, 2014-04): BAYAREALIKE+J seems to crash on some computers, usually Windows
# machines. I can't replicate this on my Mac machines, but it is almost certainly
# just some precision under-run issue, when optim/optimx tries some parameter value
# just below zero. The "min" and "max" options on each parameter are supposed to
# prevent this, but apparently optim/optimx sometimes go slightly beyond
# these limits. Anyway, if you get a crash, try raising "min" and lowering "max"
# slightly for each parameter:
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","min"] = 0.0000001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","max"] = 4.9999999
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","min"] = 0.0000001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","max"] = 4.9999999
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","min"] = 0.00001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","max"] = 0.99999
BioGeoBEARS_run_object = fix_BioGeoBEARS_params_minmax(BioGeoBEARS_run_object=BioGeoBEARS_run_object)
check_BioGeoBEARS_run(BioGeoBEARS_run_object)## [1] TRUEresfn = "Petaluridae_BAYAREALIKE+J_M0_unconstrained_v1.Rdata"
runslow = TRUE
if (runslow)
{
res = bears_optim_run(BioGeoBEARS_run_object)
res
save(res, file=resfn)
resBAYAREALIKEj = res
} else {
# Loads to "res"
load(resfn)
resBAYAREALIKEj = res
}## [1] "Note: tipranges_to_tip_condlikes_of_data_on_each_state() is converting a states_list with (0-based) numbers to the equivalent areanames"
##
## Your computer has 8 cores.
##
## Your computer has 8 cores. You have chosen to use:
## num_cores_to_use = 6 cores for the matrix exponentiations in the likelihood calculations.
## Started cluster with 6 cores.
##
## [1] "parscale:"
## [1] 5.00010 5.00010 1.00002 1.00000
##
##
## NOTE: Before running optimx(), here is a test calculation of the data likelihood
## using calc_loglike_for_optim() on initial parameter values, with printlevel=2...
## if this crashes, the error messages are more helpful
## than those from inside optimx().
##
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.542
##
## calc_loglike_for_optim() on initial parameters loglike=-12.54249
##
##
##
## Calculation of likelihood on initial parameters: successful.
##
## Now starting Maximum Likelihood (ML) parameter optimization with optimx()...
##
##
##
## Printing any warnings() that occurred during calc_loglike_for_optim():
##
## NULL
##
##
## Results of optimx_scalecheck() below. Note: sometimes rescaling parameters may be helpful for ML searches, when the parameters have much different absolute sizes. This can be attempted by setting BioGeoBEARS_run_object$rescale_params = TRUE.
##
## $lpratio
## [1] 4
##
## $lbratio
## [1] 0.6989787
##
## Maximizing -- use negfn and neggr
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.542## Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower, : Parameters or bounds appear to have different scalings.
## This can cause poor performance in optimization.
## It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.## Warning in (function (npt = min(n + 2L, 2L * n), rhobeg = NA, rhoend = NA, :
## unused control arguments ignored## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r mf
## 1 0.007 0.896 0 1 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5 0.1
## dp fdp LnL
## 1 1 0 -12.542
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.2 0.896 0 1 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -23.056
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.4 0.896 0 1 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -29.98
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.2 1.096 0 1 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -21.632
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0.2 0.896 0 0.8 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -23.053
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.2 0.896 0 1 0 0 1 0 0.4 0.6 0.6 0.6 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -23.056
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0 0.896 0 1 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -14.586
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0 1.096 0 1 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -14.586
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0 1.229 0 1 0 0 1 0 0.35 0.65 0.65 0.65 0 0 0 0 1 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -15.341
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0 1.098 0 1 0 0 1 0 0.1 0.9 0.9 0.9 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -14.64
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v
## 1 0 1.096 0 0.965 0 0 1 0 0.2 0.8 0.8 0.8 0 0 0 0 1 0 0.5
## mx01r mf dp fdp LnL
## 1 0.5 0.1 1 0 -14.577
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.05 0 0.954 0 0 1 0 0.218 0.782 0.782 0.782 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.652
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.109 0 0.969 0 0 1 0 0.215 0.785 0.785 0.785 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.635
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.097 0 0.96 0 0 1 0 0.181 0.819 0.819 0.819 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.527
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.106 0 0.931 0 0 1 0 0.155 0.845 0.845 0.845 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.481
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.126 0 0.858 0 0 1 0 0.129 0.871 0.871 0.871 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.497
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.022 1.106 0 0.931 0 0 1 0 0.155 0.845 0.845 0.845 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -15.29
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.111 0 0.912 0 0 1 0 0.143 0.857 0.857 0.857 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.479
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.118 0 0.917 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.478
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.115 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.478
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0 1.115 0 0.92 0 0 1 0 0.143 0.857 0.857 0.857 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.479
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.002 1.115 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.124
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 1.115 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.094
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 1.114 0 0.917 0 0 1 0 0.146 0.854 0.854 0.854 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.094
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 1.115 0 0.915 0 0 1 0 0.147 0.853 0.853 0.853 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.111
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 1.114 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.091
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 1.114 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.085
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.082
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.916 0 0 1 0 0.144 0.856 0.856 0.856 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.082
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.916 0 0 1 0 0.145 0.855 0.855 0.855 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.083
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.916 0 0 1 0 0.144 0.856 0.856 0.856 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.081
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.916 0 0 1 0 0.144 0.856 0.856 0.856 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.079
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.916 0 0 1 0 0.144 0.856 0.856 0.856 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.079
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.916 0 0 1 0 0.144 0.856 0.856 0.856 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.078
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.915 0 0 1 0 0.143 0.857 0.857 0.857 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.074
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.914 0 0 1 0 0.142 0.858 0.858 0.858 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.067
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.003 1.114 0 0.912 0 0 1 0 0.14 0.86 0.86 0.86 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -14.052
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.907 0 0 1 0 0.136 0.864 0.864 0.864 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14.025
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.898 0 0 1 0 0.127 0.873 0.873 0.873 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.977
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.003 1.115 0 0.878 0 0 1 0 0.11 0.89 0.89 0.89 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.885
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.841 0 0 1 0 0.075 0.925 0.925 0.925 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.888
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.114 0 0.859 0 0 1 0 0.094 0.906 0.906 0.906 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.866
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.115 0 0.859 0 0 1 0 0.093 0.907 0.907 0.907 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.81
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 1.118 0 0.858 0 0 1 0 0.094 0.906 0.906 0.906 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.736
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 1.117 0 0.853 0 0 1 0 0.089 0.911 0.911 0.911 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.709
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.005 1.118 0 0.843 0 0 1 0 0.08 0.92 0.92 0.92 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.661
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.005 1.118 0 0.821 0 0 1 0 0.062 0.938 0.938 0.938 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.583
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.004 1.118 0 0.781 0 0 1 0 0.023 0.977 0.977 0.977 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -14
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.016 1.112 0 0.821 0 0 1 0 0.062 0.938 0.938 0.938 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.892
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.117 0 0.826 0 0 1 0 0.061 0.939 0.939 0.939 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.587
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.003 1.115 0 0.822 0 0 1 0 0.058 0.942 0.942 0.942 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.842
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.112 0 0.819 0 0 1 0 0.065 0.935 0.935 0.935 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.537
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.112 0 0.821 0 0 1 0 0.066 0.934 0.934 0.934 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.542
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.114 0 0.818 0 0 1 0 0.063 0.937 0.937 0.937 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.534
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.114 0 0.818 0 0 1 0 0.062 0.938 0.938 0.938 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.52
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.008 1.114 0 0.82 0 0 1 0 0.063 0.937 0.937 0.937 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.518
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.009 1.114 0 0.82 0 0 1 0 0.062 0.938 0.938 0.938 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.535
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.008 1.114 0 0.82 0 0 1 0 0.063 0.937 0.937 0.937 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.517
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.008 1.114 0 0.82 0 0 1 0 0.063 0.937 0.937 0.937 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.515
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.114 0 0.821 0 0 1 0 0.063 0.937 0.937 0.937 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.517
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.114 0 0.821 0 0 1 0 0.063 0.937 0.937 0.937 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.515
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.114 0 0.82 0 0 1 0 0.063 0.937 0.937 0.937 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.514
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.114 0 0.82 0 0 1 0 0.063 0.937 0.937 0.937 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.512
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.114 0 0.82 0 0 1 0 0.062 0.938 0.938 0.938 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.51
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.115 0 0.82 0 0 1 0 0.062 0.938 0.938 0.938 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.505
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.115 0 0.82 0 0 1 0 0.061 0.939 0.939 0.939 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.502
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.116 0 0.819 0 0 1 0 0.06 0.94 0.94 0.94 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.498
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.116 0 0.819 0 0 1 0 0.06 0.94 0.94 0.94 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.498
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.116 0 0.819 0 0 1 0 0.06 0.94 0.94 0.94 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.498
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.116 0 0.819 0 0 1 0 0.06 0.94 0.94 0.94 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.5
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.116 0 0.819 0 0 1 0 0.06 0.94 0.94 0.94 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.497
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.116 0 0.819 0 0 1 0 0.06 0.94 0.94 0.94 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.493
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.116 0 0.819 0 0 1 0 0.059 0.941 0.941 0.941 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.486
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.116 0 0.819 0 0 1 0 0.059 0.941 0.941 0.941 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.481
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.117 0 0.819 0 0 1 0 0.059 0.941 0.941 0.941 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.478
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.117 0 0.819 0 0 1 0 0.058 0.942 0.942 0.942 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.473
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.118 0 0.818 0 0 1 0 0.057 0.943 0.943 0.943 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.466
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.119 0 0.817 0 0 1 0 0.055 0.945 0.945 0.945 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.466
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.118 0 0.818 0 0 1 0 0.057 0.943 0.943 0.943 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.466
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.118 0 0.818 0 0 1 0 0.056 0.944 0.944 0.944 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.463
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.118 0 0.818 0 0 1 0 0.056 0.944 0.944 0.944 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.472
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.118 0 0.818 0 0 1 0 0.056 0.944 0.944 0.944 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.457
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.118 0 0.818 0 0 1 0 0.055 0.945 0.945 0.945 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.447
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.118 0 0.818 0 0 1 0 0.055 0.945 0.945 0.945 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.442
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.118 0 0.817 0 0 1 0 0.054 0.946 0.946 0.946 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.438
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.118 0 0.817 0 0 1 0 0.053 0.947 0.947 0.947 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.432
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.118 0 0.818 0 0 1 0 0.052 0.948 0.948 0.948 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.44
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.118 0 0.817 0 0 1 0 0.053 0.947 0.947 0.947 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.428
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.118 0 0.816 0 0 1 0 0.052 0.948 0.948 0.948 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.423
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.119 0 0.816 0 0 1 0 0.051 0.949 0.949 0.949 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.421
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.119 0 0.816 0 0 1 0 0.051 0.949 0.949 0.949 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.414
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.007 1.12 0 0.816 0 0 1 0 0.05 0.95 0.95 0.95 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.409
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.007 1.121 0 0.815 0 0 1 0 0.048 0.952 0.952 0.952 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.413
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.008 1.12 0 0.816 0 0 1 0 0.05 0.95 0.95 0.95 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.399
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.009 1.12 0 0.816 0 0 1 0 0.05 0.95 0.95 0.95 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.405
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.008 1.121 0 0.816 0 0 1 0 0.05 0.95 0.95 0.95 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.402
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.008 1.121 0 0.816 0 0 1 0 0.05 0.95 0.95 0.95 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.399
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.121 0 0.816 0 0 1 0 0.049 0.951 0.951 0.951 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.399
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.008 1.12 0 0.816 0 0 1 0 0.049 0.951 0.951 0.951 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -13.397
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.008 1.121 0 0.816 0 0 1 0 0.049 0.951 0.951 0.951 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.391
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.121 0 0.816 0 0 1 0 0.048 0.952 0.952 0.952 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.385
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.121 0 0.815 0 0 1 0 0.047 0.953 0.953 0.953 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.373
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.122 0 0.813 0 0 1 0 0.044 0.956 0.956 0.956 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.347
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.009 1.124 0 0.809 0 0 1 0 0.038 0.962 0.962 0.962 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.296
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.128 0 0.802 0 0 1 0 0.026 0.974 0.974 0.974 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.189
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.013 1.136 0 0.789 0 0 1 0 0.002 0.998 0.998 0.998 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.94
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.013 1.137 0 0.787 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.92
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.139 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.914
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.138 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.915
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.138 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.917
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.138 0 0.787 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.916
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.139 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.918
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.138 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.914
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.138 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.914
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.138 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.914
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.138 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.914
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.138 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.914
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.138 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.914
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.139 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.913
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.139 0 0.788 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.912
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.14 0 0.789 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.911
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.143 0 0.789 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.909
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.147 0 0.791 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.904
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.156 0 0.794 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.894
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.173 0 0.8 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.873
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.209 0 0.811 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.853
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.015 1.243 0 0.824 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.834
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.244 0 0.823 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.81
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.013 1.244 0 0.823 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.8
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.244 0 0.824 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.799
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.248 0 0.825 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.795
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.257 0 0.828 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.785
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.012 1.275 0 0.834 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.77
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.013 1.31 0 0.846 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.744
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.013 1.345 0 0.858 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.717
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.013 1.415 0 0.882 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.688
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.485 0 0.906 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.722
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.013 1.415 0 0.882 0 0 1 0 0.029 0.971 0.971 0.971 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.202
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.388 0 0.885 0 0 1 0 0.025 0.975 0.975 0.975 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -13.037
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.027 1.414 0 0.884 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -13.862
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.017 1.422 0 0.865 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.886
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.013 1.408 0 0.879 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.691
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.014 1.411 0 0.876 0 0 1 0 0.006 0.994 0.994 0.994 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.858
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.013 1.42 0 0.883 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.689
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.417 0 0.878 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.754
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.014 1.415 0 0.882 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.757
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.416 0 0.881 0 0 1 0 0.001 0.999 0.999 0.999 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.659
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.414 0 0.881 0 0 1 0 0.002 0.998 0.998 0.998 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.687
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.415 0 0.881 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.651
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.416 0 0.88 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.648
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.415 0 0.88 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.649
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.416 0 0.88 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.65
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.417 0 0.881 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.647
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.418 0 0.881 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.647
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.42 0 0.882 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.646
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.422 0 0.882 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.644
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.427 0 0.884 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.643
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.425 0 0.883 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.645
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y
## 1 0.011 1.427 0 0.883 0 0 1 0 0.001 0.999 0.999 0.999 0 0 0 0 1
## mx01s mx01v mx01r mf dp fdp LnL
## 1 0 0.5 0.5 0.1 1 0 -12.653
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.427 0 0.883 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.645
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.426 0 0.884 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.643
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.427 0 0.884 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.64
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.428 0 0.884 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.639
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.431 0 0.885 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.637
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.433 0 0.885 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.636
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.438 0 0.887 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.633
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.448 0 0.89 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.635
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.438 0 0.888 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.638
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.438 0 0.888 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.631
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.438 0 0.888 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.631
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.439 0 0.888 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.63
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.441 0 0.889 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.629
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.441 0 0.889 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.628
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.444 0 0.89 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.627
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.449 0 0.891 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.624
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.459 0 0.894 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.624
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s
## 1 0.009 1.449 0 0.89 0 0 1 0 0.001 0.999 0.999 0.999 0 0 0 0 1 0
## mx01v mx01r mf dp fdp LnL
## 1 0.5 0.5 0.1 1 0 -12.672
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.009 1.449 0 0.891 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.647
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.448 0 0.892 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.623
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.446 0 0.891 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.624
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.448 0 0.892 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.63
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.447 0 0.891 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.624
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.448 0 0.892 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.627
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.448 0 0.891 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.623
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.448 0 0.892 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.622
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.448 0 0.892 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.622
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.448 0 0.892 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.622
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.448 0 0.892 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.622
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.448 0 0.892 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.621
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.449 0 0.892 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.621
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.449 0 0.892 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.621
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.449 0 0.893 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.62
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.45 0 0.893 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.62
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.451 0 0.894 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.619
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.618
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.618
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.618
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.617
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.452 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.617
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.626
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.009 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.633
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.618
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.62
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.617
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.598 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.596
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.307 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.639
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.525 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.605
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.38 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.626
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.489 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.61
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.416 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.621
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.471 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.613
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.434 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.618
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.985 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.546
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.806 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.903
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.94 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.558
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.85 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.728
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.917 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.58
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.873 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.664
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.906 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.596
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.884 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.638
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.617
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.614
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.598 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.605
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.009 1.307 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.654
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.525 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.607
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.38 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.631
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.489 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.61
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.416 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.622
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.471 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.613
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.434 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.618
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.985 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.618
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.009 1.453 0 0.806 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -13.005
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.94 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.576
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.85 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.752
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.917 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.585
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.873 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.67
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.906 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.597
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.884 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.64
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.598 0 0.985 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.527
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.307 0 0.806 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.927
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.525 0 0.94 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.548
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.38 0 0.85 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.739
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.489 0 0.917 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.575
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.416 0 0.873 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.67
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.471 0 0.906 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.594
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.434 0 0.884 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.641
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.628
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.009 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.632
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.618
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.619
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.011 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.598 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.598
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.307 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.637
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.525 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.606
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.38 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.626
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.489 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.611
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.416 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.62
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.471 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.613
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.434 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.618
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.985 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.548
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.806 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.902
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.94 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.559
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.85 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.727
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.917 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.581
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.873 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.664
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.906 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.596
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.884 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.638
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.452 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.617
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.614
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.616
## d e a b x n w u j ysv ys y s v mx01 mx01j mx01y mx01s mx01v mx01r
## 1 0.01 1.453 0 0.895 0 0 1 0 0 1 1 1 0 0 0 0 1 0 0.5 0.5
## mf dp fdp LnL
## 1 0.1 1 0 -12.615
##
##
## This is the output from optim, optimx, or GenSA. Check the help on those functions to
## interpret this output and check for convergence issues:
##
## p1 p2 p3 p4 value fevals gevals niter
## bobyqa 0.01029984 1.452609 0.8950809 1e-05 -12.61533 200 NA NA
## convcode kkt1 kkt2 xtime
## bobyqa 0 FALSE TRUE 3.824
##
##
## Stopping cluster with 6 cores.pdffn = "Petaluridae_BAYAREALIKE_vs_BAYAREALIKE+J_M0_unconstrained_v1.pdf"
pdf(pdffn, height=6, width=6)
#######################################################
# Plot ancestral states - BAYAREALIKE
#######################################################
analysis_titletxt ="BioGeoBEARS BAYAREALIKE on Petaluridae M0_unconstrained"
# Setup
results_object = resBAYAREALIKE
scriptdir = np(system.file("extdata/a_scripts", package="BioGeoBEARS"))
# States
res2 = plot_BioGeoBEARS_results(results_object, analysis_titletxt, addl_params=list("j"), plotwhat="text", label.offset=0.45, tipcex=0.7, statecex=0.7, splitcex=0.6, titlecex=0.8, plotsplits=TRUE, cornercoords_loc=scriptdir, include_null_range=TRUE, tr=tr, tipranges=tipranges)
# Pie chart
plot_BioGeoBEARS_results(results_object, analysis_titletxt, addl_params=list("j"), plotwhat="pie", label.offset=0.45, tipcex=0.7, statecex=0.7, splitcex=0.6, titlecex=0.8, plotsplits=TRUE, cornercoords_loc=scriptdir, include_null_range=TRUE, tr=tr, tipranges=tipranges)## LnL nparams d e b j
## 1 -12.54107 4 0.007421225 0.8957392 1 1e-05#######################################################
# Plot ancestral states - BAYAREALIKE+J
#######################################################
analysis_titletxt ="BioGeoBEARS BAYAREALIKE+J on Petaluridae M0_unconstrained"
# Setup
results_object = resBAYAREALIKEj
scriptdir = np(system.file("extdata/a_scripts", package="BioGeoBEARS"))
# States
res1 = plot_BioGeoBEARS_results(results_object, analysis_titletxt, addl_params=list("j"), plotwhat="text", label.offset=0.45, tipcex=0.7, statecex=0.7, splitcex=0.6, titlecex=0.8, plotsplits=TRUE, cornercoords_loc=scriptdir, include_null_range=TRUE, tr=tr, tipranges=tipranges)
# Pie chart
plot_BioGeoBEARS_results(results_object, analysis_titletxt, addl_params=list("j"), plotwhat="pie", label.offset=0.45, tipcex=0.7, statecex=0.7, splitcex=0.6, titlecex=0.8, plotsplits=TRUE, cornercoords_loc=scriptdir, include_null_range=TRUE, tr=tr, tipranges=tipranges)## LnL nparams d e b j
## 1 -12.61533 4 0.01029984 1.452609 0.8950809 1e-05dev.off()## pdf
## 3cmdstr = paste("open ", pdffn, sep="")
system(cmdstr)restable = NULL
teststable = NULL
#######################################################
# Statistics -- DEC vs. DEC+J
#######################################################
# We have to extract the log-likelihood differently, depending on the
# version of optim/optimx
LnL_2 = get_LnL_from_BioGeoBEARS_results_object(resDEC)
LnL_1 = get_LnL_from_BioGeoBEARS_results_object(resDECj)
LnL_1## [1] -12.75508LnL_2## [1] -15.13797numparams1 = 3
numparams2 = 2
stats = AICstats_2models(LnL_1, LnL_2, numparams1, numparams2)
stats## alt null LnLalt LnLnull DFalt DFnull DF Dstatistic
## 1 -12.755083957688 -15.137968836522 3 2 1 4.76576975766805
## pval test tail AIC1 AIC2 AICwt1
## 1 0.0290310748144794 chi-squared one-tailed 31.51017 34.27594 0.7994539
## AICwt2 AICweight_ratio_model1 AICweight_ratio_model2
## 1 0.2005461 3.986385 0.2508538# DEC, null model for Likelihood Ratio Test (LRT)
res2 = extract_params_from_BioGeoBEARS_results_object(results_object=resDEC, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
# DEC+J, alternative model for Likelihood Ratio Test (LRT)
res1 = extract_params_from_BioGeoBEARS_results_object(results_object=resDECj, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
res2$b=1
rbind(res2, res1)## LnL numparams d e j b
## 1 -15.13797 2 0.003073225 0.06042132 0.0000e+00 1.0000000
## 2 -12.75508 4 0.006892910 0.47867678 4.5599e-05 0.9999669tmp_tests = conditional_format_table(stats)
restable = rbind(restable, res2, res1)
teststable = rbind(teststable, tmp_tests)
#######################################################
# Statistics -- DIVALIKE vs. DIVALIKE+J
#######################################################
# We have to extract the log-likelihood differently, depending on the
# version of optim/optimx
LnL_2 = get_LnL_from_BioGeoBEARS_results_object(resDIVALIKE)
LnL_1 = get_LnL_from_BioGeoBEARS_results_object(resDIVALIKEj)
numparams1 = 3
numparams2 = 2
stats = AICstats_2models(LnL_1, LnL_2, numparams1, numparams2)
stats## alt null LnLalt LnLnull DFalt DFnull DF
## 1 -12.5006906974205 -12.6235597513041 3 2 1
## Dstatistic pval test tail AIC1 AIC2
## 1 0.245738107767011 0.620092124284377 chi-squared one-tailed 31.00138 29.24712
## AICwt1 AICwt2 AICweight_ratio_model1 AICweight_ratio_model2
## 1 0.2937727 0.7062273 0.4159747 2.403993# DIVALIKE, null model for Likelihood Ratio Test (LRT)
res2 = extract_params_from_BioGeoBEARS_results_object(results_object=resDIVALIKE, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
# DIVALIKE+J, alternative model for Likelihood Ratio Test (LRT)
res1 = extract_params_from_BioGeoBEARS_results_object(results_object=resDIVALIKEj, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
rbind(res2, res1)## LnL numparams d e b j
## 1 -12.62356 4 0.007527682 0.6976567 1 1e-05
## 2 -12.50069 4 0.007455278 1.1048796 1 1e-05conditional_format_table(stats)## alt null LnLalt LnLnull DFalt DFnull DF Dstatistic pval test
## 1 -12.5 -12.62 3 2 1 0.25 0.62 chi-squared
## tail AIC1 AIC2 AICwt1 AICwt2 AICweight_ratio_model1
## 1 one-tailed 31 29.25 0.29 0.71 0.42
## AICweight_ratio_model2
## 1 2.4tmp_tests = conditional_format_table(stats)
restable = rbind(restable, res2, res1)
teststable = rbind(teststable, tmp_tests)
#######################################################
# Statistics -- BAYAREALIKE vs. BAYAREALIKE+J
#######################################################
# We have to extract the log-likelihood differently, depending on the
# version of optim/optimx
LnL_2 = get_LnL_from_BioGeoBEARS_results_object(resBAYAREALIKE)
LnL_1 = get_LnL_from_BioGeoBEARS_results_object(resBAYAREALIKEj)
numparams1 = 3
numparams2 = 2
stats = AICstats_2models(LnL_1, LnL_2, numparams1, numparams2)
stats## alt null LnLalt LnLnull DFalt DFnull DF
## 1 -12.6153260026673 -12.5410718256132 3 2 1
## Dstatistic pval test tail AIC1 AIC2 AICwt1
## 1 -0.148508354108163 1 chi-squared one-tailed 31.23065 29.08214 0.2545949
## AICwt2 AICweight_ratio_model1 AICweight_ratio_model2
## 1 0.7454051 0.3415524 2.927808# BAYAREALIKE, null model for Likelihood Ratio Test (LRT)
res2 = extract_params_from_BioGeoBEARS_results_object(results_object=resBAYAREALIKE, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
# BAYAREALIKE+J, alternative model for Likelihood Ratio Test (LRT)
res1 = extract_params_from_BioGeoBEARS_results_object(results_object=resBAYAREALIKEj, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
rbind(res2, res1)## LnL numparams d e b j
## 1 -12.54107 4 0.007421225 0.8957392 1.0000000 1e-05
## 2 -12.61533 4 0.010299836 1.4526095 0.8950809 1e-05conditional_format_table(stats)## alt null LnLalt LnLnull DFalt DFnull DF Dstatistic pval test
## 1 -12.62 -12.54 3 2 1 -0.15 1 chi-squared
## tail AIC1 AIC2 AICwt1 AICwt2 AICweight_ratio_model1
## 1 one-tailed 31.23 29.08 0.25 0.75 0.34
## AICweight_ratio_model2
## 1 2.93tmp_tests = conditional_format_table(stats)
restable = rbind(restable, res2, res1)
teststable = rbind(teststable, tmp_tests)
#########################################################################
# ASSEMBLE RESULTS TABLES: DEC, DEC+J, DIVALIKE, DIVALIKE+J, BAYAREALIKE, BAYAREALIKE+J
#########################################################################
#teststable$alt = c("DEC+J", "DIVALIKE+J", "BAYAREALIKE+J")
#teststable$null = c("DEC", "DIVALIKE", "BAYAREALIKE")
row.names(restable) = c("DEC", "DEC+J", "DIVALIKE", "DIVALIKE+J", "BAYAREALIKE", "BAYAREALIKE+J")
restable = put_jcol_after_ecol(restable)
restable## LnL numparams d e j b
## DEC -15.13797 2 0.003073225 0.06042132 0.0000e+00 1.0000000
## DEC+J -12.75508 4 0.006892910 0.47867678 4.5599e-05 0.9999669
## DIVALIKE -12.62356 4 0.007527682 0.69765669 1.0000e-05 1.0000000
## DIVALIKE+J -12.50069 4 0.007455278 1.10487956 1.0000e-05 1.0000000
## BAYAREALIKE -12.54107 4 0.007421225 0.89573918 1.0000e-05 1.0000000
## BAYAREALIKE+J -12.61533 4 0.010299836 1.45260946 1.0000e-05 0.8950809# Look at the results!!
restable## LnL numparams d e j b
## DEC -15.13797 2 0.003073225 0.06042132 0.0000e+00 1.0000000
## DEC+J -12.75508 4 0.006892910 0.47867678 4.5599e-05 0.9999669
## DIVALIKE -12.62356 4 0.007527682 0.69765669 1.0000e-05 1.0000000
## DIVALIKE+J -12.50069 4 0.007455278 1.10487956 1.0000e-05 1.0000000
## BAYAREALIKE -12.54107 4 0.007421225 0.89573918 1.0000e-05 1.0000000
## BAYAREALIKE+J -12.61533 4 0.010299836 1.45260946 1.0000e-05 0.8950809teststable## alt null LnLalt LnLnull DFalt DFnull DF Dstatistic pval test
## 1 -12.76 -15.14 3 2 1 4.77 0.029 chi-squared
## 11 -12.5 -12.62 3 2 1 0.25 0.62 chi-squared
## 12 -12.62 -12.54 3 2 1 -0.15 1 chi-squared
## tail AIC1 AIC2 AICwt1 AICwt2 AICweight_ratio_model1
## 1 one-tailed 31.51 34.28 0.80 0.20 3.99
## 11 one-tailed 31 29.25 0.29 0.71 0.42
## 12 one-tailed 31.23 29.08 0.25 0.75 0.34
## AICweight_ratio_model2
## 1 0.25
## 11 2.4
## 12 2.93#######################################################
# Save the results tables for later -- check for e.g.
# convergence issues
#######################################################
# Loads to "restable"
save(restable, file="restable_v1.Rdata")
load(file="restable_v1.Rdata")
# Loads to "teststable"
save(teststable, file="teststable_v1.Rdata")
load(file="teststable_v1.Rdata")
# Also save to text files
write.table(restable, file="restable.txt", quote=FALSE, sep="\t")
#write.table(unlist_df(teststable), file="teststable.txt", quote=FALSE, sep="\t")
#######################################################
# Model weights of all six models
#######################################################
restable2 = restable
# With AICs:
AICtable = calc_AIC_column(LnL_vals=restable$LnL, nparam_vals=restable$numparams)
restable = cbind(restable, AICtable)
restable_AIC_rellike = AkaikeWeights_on_summary_table(restable=restable, colname_to_use="AIC")
restable_AIC_rellike = put_jcol_after_ecol(restable_AIC_rellike)
restable_AIC_rellike## LnL numparams d e j b
## DEC -15.13797 2 0.003073225 0.06042132 0.0000e+00 1.0000000
## DEC+J -12.75508 4 0.006892910 0.47867678 4.5599e-05 0.9999669
## DIVALIKE -12.62356 4 0.007527682 0.69765669 1.0000e-05 1.0000000
## DIVALIKE+J -12.50069 4 0.007455278 1.10487956 1.0000e-05 1.0000000
## BAYAREALIKE -12.54107 4 0.007421225 0.89573918 1.0000e-05 1.0000000
## BAYAREALIKE+J -12.61533 4 0.010299836 1.45260946 1.0000e-05 0.8950809
## AIC AIC_wt
## DEC 34.27594 0.1048940
## DEC+J 33.51017 0.1538280
## DIVALIKE 33.24712 0.1754509
## DIVALIKE+J 33.00138 0.1983887
## BAYAREALIKE 33.08214 0.1905371
## BAYAREALIKE+J 33.23065 0.1769014# With AICcs -- factors in sample size
samplesize = length(tr$tip.label)
AICtable = calc_AICc_column(LnL_vals=restable$LnL, nparam_vals=restable$numparams, samplesize=samplesize)
restable2 = cbind(restable2, AICtable)
restable_AICc_rellike = AkaikeWeights_on_summary_table(restable=restable2, colname_to_use="AICc")
restable_AICc_rellike = put_jcol_after_ecol(restable_AICc_rellike)
restable_AICc_rellike## LnL numparams d e j b
## DEC -15.13797 2 0.003073225 0.06042132 0.0000e+00 1.0000000
## DEC+J -12.75508 4 0.006892910 0.47867678 4.5599e-05 0.9999669
## DIVALIKE -12.62356 4 0.007527682 0.69765669 1.0000e-05 1.0000000
## DIVALIKE+J -12.50069 4 0.007455278 1.10487956 1.0000e-05 1.0000000
## BAYAREALIKE -12.54107 4 0.007421225 0.89573918 1.0000e-05 1.0000000
## BAYAREALIKE+J -12.61533 4 0.010299836 1.45260946 1.0000e-05 0.8950809
## AICc AICc_wt
## DEC 35.99022 0.73083534
## DEC+J 41.51017 0.04625714
## DIVALIKE 41.24712 0.05275930
## DIVALIKE+J 41.00138 0.05965686
## BAYAREALIKE 41.08214 0.05729584
## BAYAREALIKE+J 41.23065 0.05319550# Also save to text files
write.table(restable_AIC_rellike, file="restable_AIC_rellike.txt", quote=FALSE, sep="\t")
write.table(restable_AICc_rellike, file="restable_AICc_rellike.txt", quote=FALSE, sep="\t")
# Save with nice conditional formatting
write.table(conditional_format_table(restable_AIC_rellike), file="restable_AIC_rellike_formatted.txt", quote=FALSE, sep="\t")
write.table(conditional_format_table(restable_AICc_rellike), file="restable_AICc_rellike_formatted.txt", quote=FALSE, sep="\t")